Breeding and Genetics
View abstracts in the conference PDF booklet.
Novel Loci fsd6.1 and csgl3 Regulate Ultra-high Fruit Spine Density in Cucumber
Kailiang Bo, Han Miao, Min Wang, Xiaoxiao Xie, Zichao Song, Qing Xie, Lixue Shi, Weiping Wang, Shuang Wei, Shengping Zhang, Xingfang Gu
Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
Fruit spine density, a domestication trait, largely influences the commercial value of cucumbers. However, the molecular basis of fruit spine density in cucumber remains unclear. In this study, four populations were derived from five materials, which included three with low fruit spine density, one with high fruit spine density, and one with ultra-high fruit spine density. Fruit spine densities were measured in 15 environments over a span of six years. The distributions were bimodal, suggesting that fruit spine density is controlled by a major-effect QTL. QTL analysis determined that the same major-effect QTL, fsd6.2, is present in four populations. Fine- mapping indicated that Csgl3 is the candidate gene of the fsd6.2 locus. Phylogenetic and geographical distribution analyses revealed that Csgl3 originated from China, which has the highest genetic diversity for fruit spine density. One novel minor-effect QTL, fsd6.1, was detected in the HR and HP populations derived from the cross between 65G and 02245. In addition, GWAS identified a novel locus that coincides with fsd6.1. Inspection of a candidate region of about 18 kb in size using pairwise LD correlations, combined with genetic diversity and phylogenetic analysis of fsd6.1 in natural populations, indicated that Csa6G421750 is the candidate gene responsible for ultra-high fruit spine density in cucumber. This study provides new insights into the origin of fruit spine density and the evolution of high/ultra-high fruit spine density during cucumber domestication.
Genomics-Enabled Genetic Mapping and Marker Development of Disease Resistance Loci in Melon and Watermelon
Sandra Branham¹, Amnon Levi¹, Zhangjun Fei², W. Patrick Wechter¹
¹U.S. Department of Agriculture, Agricultural Research Service, U.S. Vegetable Laboratory, Charleston, SC, USA. ²Boyce Thompson Institute, Ithaca, NY, USA
Incorporation of disease resistance into elite cultivars is one of the main goals of most crop breeding programs. Development of markers for disease resistance loci can facilitate crop improvement through gene pyramiding, selection for resistance to multiple diseases in a single generation, large-scale germplasm screening, and potentially, gene editing. Marker development in plants is a multi-faceted process which includes resistance germplasm discovery, robust and accurate phenotyping, genotyping, development of segregating populations, narrowing of resistance-associated genetic regions, and finally validation of markers in actual breeding schemes. Here we present a combination of techniques (QTL- mapping, GWAS, QTL-seq, and marker development) that we are using to identify disease resistance loci (primarily for Fusarium wilt) in watermelon and melon by leveraging genome- level data. Partial Funding provided by the Specialty Crop Block Grant Program at the U.S. Department of Agriculture (USDA) through Grant 14-SCBGP-CA-0006 (The CucCAP Project)
Identification and Mapping of a Dwarfness Related Gene in Watermelon (Citrullus lanatus) by Steps Mapping
Namfon Chomkaeo1, Darush Struss1, Chotipa Sakulsingharoj², Saengtong Pongjaroenkit²
¹Department of Biotechnology, East West Seed Company, Chiangmai, Sansai, Thailand. ²Program in Genetics, Faculty of Science, Maejo University, Chiangmai, Sansai, Thailand
Dwarf habit or dwarfism is a desired agronomic trait in watermelon, as it allows higher plant density than is feasible for the standard indeterminate, trailing type, and thereby increases yield as well as the decreasing soil disease and labor required to cultivate. Dwarf growth habit in watermelon is controlled by the simply inherited, recessive gene (dw-1). The plant hormone gibberellin (GA) regulates plant growth, including stem elongation. Numerous genes are involved in gibberellin and gibberellin precursor biosynthesis pathway, which is distributed across the watermelon genome. We used a new approach, “Steps mapping” to map dw-1. This approach consists of conventional mapping followed by using the reference genome and gene annotation information for fine mapping. The candidate dw-1 was mapped in a F2 watermelon population (n=309) derived from inbred watermelon lines KK-6939 (trailing growth habit) and TH-15974 (dwarf growth habit). Molecular mapping was conducted using single nucleotide polymorphisms (SNPs) markers. A genetic map was constructed consisting of 56 SNP loci in 11 linkage groups (chromosomes). Linkage analysis placed dw-1 at the top of watermelon chromosome 9. Molecular marker “WMSNP-9-88” co-segregated with dw-1 and was 24.4 cM away from dw-1. The high-density genetic map was used to identify genomic regions highly associated with dw-1, and a new marker, “WMSNP-0002780,” was tightly linked to dw-1, with a genetic distance of 0.8 cM, and physical map distance ca. 1.9 Mb. Two candidate genes including Cla015407 and Cla015408, located on chromosome 9 with a physical map distance ca. 1.8 Mb. were detected. Both genes encode a protein predicted to be a gibberellin 3-beta- hydroxylase protein, which is a catalyst in gibberellin biosynthesis III (early C-13 hydroxylation) pathway. For the controls, GA20 was metabolized to GA1, which is the active form that affects stem elongation in plants.
Evaluation of Watermelon Germplasm in Texas, a Genotype-By-Environment Study on Yield and Path Analysis on Associated Traits
Edgar Correa¹, Subas Malla², Carlos Avila³, Kevin Crosby¹
¹Texas A&M University, College Station, USA. ²Texas A&M AgriLife Research & Extension, Uvalde, USA. ³Texas A&M AgriLife Research & Extension, Weslaco, USA
In 2017, Texas was one of the top five watermelon producing states with 0.36 Mt harvested, but it lagged behind other top producing states in productivity (40 t ha-1). The objectives of this study were to 1) evaluate 42 germlines, including 6 commercial checks, comprising of Texas A&M (TAM) and selected U.S. National Plant Germplasm System at College Station, TX and Uvalde, TX in 2018, and 2) understand the effect of yield components on yield. Phenotypic traits measured were total yield (TY), sugar content (SC), rind thickness (RT), fruit length (FL), number (FN), circumference (CIR), weight (FW), and firmness (FRM). An analysis of variance showed significant interaction (P < 0.05) between genotype and environment for TY, SC, RT, FN, and FRM. In a “Which Won Where” genotype, genotype-by-trait (GGT) biplot, TY, FL, CIR, and FW were grouped together in the ‘Jubilee’ sector. Within that sector there were F1 hybrids and purelines; ‘Chubby Gray’, ‘Sunshade’, ‘Charleston Gray’, and ‘Calhoun Gray’. The GGE biplot analysis for TY showed that, TAM2 and ‘Pathfinder’ (F1) were superior germplasm in Uvalde, whereas ‘Desert King’ and ‘Big Striped’ (F1) were superior germplasm in College Station. A “Mean vs. Stability” GGE biplot showed ‘Desert King’ and ‘Jubilee’ as the most unstable, while ‘Chubby Gray’ and ‘Charleston Gray’ as stable. For SC, TAM 4 and ‘Dixielee’ performed superior in College Station and Uvalde, respectively. Path analysis showed a positive direct effect from FN (0.62), FL (0.65), CIR (0.46), and FW (0.22) on TY. This indicates that although one may select for FN, other traits such as CIR, FL, and FW will also influence TY. The path analysis also showed a negative direct effect from SC (-0.17), indicating that solely selecting for SC may deter the increase of TY. This information will aid in selecting germplasm adapted to Texas for parental use in cultivar development.
Mission Melon: Improving Qualitative traits in Cucumis melo using Phenomics
Ashlynn Fix¹, Jeekin Lau², Kevin Crosby ², Bhimagouda Patil 3, Daniel Leskovar 4, William Rooney5, Wayne Smith5
1Department of Horticultural Science and Plant Breeding, Texas A&M University , College Station, Texas, USA. ²Department of Horticultural Sciences, Texas A&M University , College Station, Texas, USA. 3Vegetable and Fruit Improvement Center, Texas A&M University , College Station, Texas, USA. 4Department of Horticultural Sciences, Texas A&M AgriLife Research & Extension Center, Uvalde, USA. 5Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas, USA
Muskmelon is a diploid, monoecious, annual species in the Cucurbitaceae family with origins in India, primarily cultivated for its numerous culinary usages and nutritional benefits. The United States ranks fourth internationally for melon production, with a 300-million-dollar market and 90-thousand acres farmed yearly. The objective of this study was to address producer and consumer needs’ in a dynamic market by developing melon hybrid cultivars with enhanced fruit quality and yield through the breeding of F1 hybrids from elite inbred lines. Nineteen hybrids and twenty-three elite inbred lines were evaluated in Uvalde, Texas under irrigated (control) and drought conditions. Range of qualitative traits evaluated: weight (lbs.), firmness (N), and percent total soluble solids (% TSS) were from 1.8 – 14.2 lbs., 17.3 – 134 N, and 4.8 – 15.6 % TSS under the control treatment; 2.1 – 14.3 lbs., 11 – 131 N, and 6.7 – 15.1 % TSS under the drought treatment. Experiments for this study were analyzed using statistical software (JMP Pro 13.0.0.), with a REML model = σfamily + σenvironment + σrep[environment] + σfamily x environment + σerror, to find the variance for each trait. These variances were then used to calculate the broad-sense heritability (σfamily / σfamily + σfamily x environment + σerror). Measured heritability estimates for qualitative traits were relatively low: a*, 0.4584; b*, 0.2506; weight, 0.2513; size, 0.2204; color, 0.2454. An analysis determined there is a biological explanation for the positive correlation in qualitative traits, as well as identified a useful hybrid (BL 110 x BL 109). Under the control treatment, % TSS high-parent heterosis ranged from -35.78 to 16.83; drought treatment % TSS heterosis ranged from -16.16 to 18.67. Due to the lack of a complete factorial experimental design, specific combining ability was not determinable. This study was supported by United States Department of Agriculture-NIFA-SCRI- 2017-51181-26834 through the National Center of Excellence for Melon at the Vegetable and Fruit Improvement Center of Texas A&M University.
Study on the Development of Tubercules and Spines in Cucumber
Gang Wang, Huanle He, Junsong Pan, Run Cai
School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
The cucumber(Cucumis sativus L.) fruit contains tubercules and spines on the surface, which is an extremely valuable quality trait affecting the selection of customers. Cucumber fruit tubercules are derived from an increase in cell numbers by division of several layers of cells that lie near the fruit spine-base cells. Cucumber fruit spines are multicellular, non-glandular trichomes developed from epidermal cells of the fruit skin, and are similar in shape and structure to leaf trichomes. The tubercules and spines affect the cleaning, packaging, transportation, and storage of cucumber fruits. Therefore, study of the development and regulation of tubercules and spines will improve breeding and enhance the economic value of cucumber production. In past few years, we isolated three genes involved in development of cucumber tubercules and spines by map-based cloning, including tuberculate fruit gene (Tu), trichome-less (Tril), and Micro-trichome (Mict). The genetic analysis showed that Tu, a single dominant gene, controls the development of tuberculates. Tu encodes a transcription factor with a single C2H2 zinc finger domain. Our results suggested that Tu probably caused the fruit tubercules formation by promoted CTK biosynthesis in fruit warts. The mict, a micro-trichome mutant, is controlled by a single recessive gene in the nucleus. Mict encodes a class I homeodomain-leucine zipper (HD-Zip) transcription factor involved in multicellular trichome development. The tril is a mutant which has no spines on the surface of cucumber fruit. Genetic analysis revealed that Tril is inherited as a dominant trait at a single locus and controls the initiation of cucumber trichomes/fruit spines. Tril encodes Protodermal factor (PDF) which is a member of class IV homeodomain-leucine zipper (HD-Zip IV) family. Tril not only could control the initiation of cucumber trichomes/spines, but also involved the later development of trichomes/spines including the aspect of density and structure. The genetic analysis showed that Tril is recessive epistatic to the Mict and Mict is recessive epistatic to Tu. Next, we will analyze the regulation relationship among Tril, Mict, and Tu and how they regulate coordinately the development of tubercules and spines in cucumber.
Production and Characterization of Bitter Gourd Derived From Intraspecific Hybridization
Muhammad Ghani1, Muhammad Amjad¹, Khurram Ziaf¹, Muhammad Abbas¹, Aamir Khan²
¹Institute of Horticultural Sciences, University of Agriculture Faisalabad, Faisalabad, Punjab, 38040, Pakistan. ²Department of Horticulture Sciences, Bahauddin Zakariya University, Multan, Punjab, Pakistan
Bitter gourd (Momordica charantia L.) is an important vegetable crop in Pakistan. It is consisting of two famous local varieties, M. charantia var. charantia, which produces large fusiform fruits, and M. charantia var. muricata, a wild variety with small and round fruits. However, these two varieties have not fulfilled the required demand of farmers due to the lack of disease and pest resistance, and low yield. Many companies have imported seed from other countries, but they were not suitable our local climate and created many new production problems. This problem can be solved by the intraspecific hybridization in bitter gourd. Therefore, we made the intraspecific crosses among different bitter gourd genotypes. The maximum number of seed per fruit was found in the combination of MC27 x MC23. While, the highest seed yield was observed in the combination of MC23 x MC27. Hybrid combination MC24 x MC23 had the maximum number of pistillate flower node and number of fruit per plant, and the fewest days to maturity. The fruit length and width were maximum in hybrid MC24 x MC27, while ovary length and width were maximum in hybrid MC27 x MC23. Furthermore, the fruit weight and yield per plant was highest in combination MC24 x MC1. So, this hybrid has improved the sustainable production of Bitter gourd. It has also increased the food supply and reduce the hunger in the Pakistan.
Dissecting Multiflower Male Truss Character in Melon (Cucumis melo L.)
Ana Garcés¹, Julia Malo1, Maria Gomez-Guillamon²
¹Centro de Investigación y Tecnología Agroalimentaria de Aragón. Instituto Agroalimentario de Aragón – IA2 (CITA-Universidad de Zaragoza), Zaragoza, Spain. ²Institute of Subtropical and Mediterranean Hortofruticulture La Mayora, UMA-CSIC., Algarrobo, Malaga, Spain
Male flowers in melon are usually found alone or in groups of 1-3 flowers per node. However, Zimbabwean melon line TGR-1551 has been identified to exhibit multiflower male trusses. In a previous study, one major QTL on linkage group 6 associated with the character in a poorly saturated region of a map of a RIL population derived from a cross between TGR-1551 and the Spanish melon cultivar ‘Bola de Oro’. Now, a dissection of the character through the construction of a high-density map and the addition of one more phenotypic character has been carried out. High resolution QTL analysis was performed using genotyping by sequencing (GBS) of the same RIL population derived from the cross between TGR-1551 and ‘Bola de Oro’. Genotypic data included approximately 1600 SNP markers and phenotypic data were based on the presence or absence of multiflower male trusses in 2012, 2013, and 2014 evaluations. In 2014, the number of flowers/node in the RIL population was also recorded. A major QTL on chromosome 6 (LOD score 12.89 for 2012, 19.9 for 2013, and 22.7 for 2014), which could explain up to 51.7 % of the phenotypic variability observed for multiflower male truss has been confirmed; the same QTL has been also identified for the number of flowers per node (LOD score 6.64 and R2 17.4). This QTL collocated with the QTL described in our previous study although this time the level of phenotypic variation explained was higher and the stability of the character across three years has been confirmed. In addition, other two minor QTLs on chromosomes 6 and 4 were detected, explaining 7.1% and 9.5% of the phenotypic variance respectively. While the candidate gene MELO3C006888 had already been detected in our previous study, three novel candidates genes (MELO3C006880, MELO3C006860, and MELO3C006940) have been identified in the same QTL region. Further research through gene sequencing and gene expression profiling is needed to confirm the exact role of the found candidate genes on the character.
Genome-Wide Association Studies of Important Agronomic Traits in Watermelon
Shaogui Guo1,², Xin Wang², Shan Wu², Honghe Sun¹, Shengjie Zhao³, Yi Ren¹, Jie Zhang¹, Guoyi Gong¹, Haiying Zhang¹, Wenge Liu³, Zhangjun Fei², Yong Xu¹
¹Beijing Vegetable Research Center of Beijing Academy of Agriculture and Forestry Sciences, Beijing, China. ²Boyce Thompson Institute, Ithaca, USA. ³Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
Watermelon is an important economic crop throughout the world. Molecular assisted breeding is a powerful approach to facilitate the variety improvement. Compared with field crops, knowledge of genomic loci associated with important horticultural traits in watermelon is limited. We performed genome-wide association studies (GWAS) of seven agronomic traits, including flesh sweetness, flesh bitterness, flesh color, seed color, rind color, rind stripe and the resistance to Fusarium oxysporum race 1, using a population containing 415 watermelon accessions. A genome region on chromosome 2 was identified to be significantly associated with flesh sweetness, and a tonoplast sugar transporter gene in this region was identified as the candidate gene. For flesh bitterness, a region on chromosome 1 was identified, which contains the candidate gene encoding a BHLH transcription factor. For flesh color, a region on chromosome 4 and a lycopene beta-cyclase gene in this region were identified. For Fusarium oxysporum race 1 resistance, a significantly associated region was identified on chromosome 1 containing a potential candidate gene encoding an acidic endochitinase. In addition, genome regions highly associated with seed color, rind color and rind stripe were also identified through our GWAS analyses. The identified genome regions and the candidate genes highly associated with important agronomic traits provide valuable resources for molecular assisted breeding in watermelon.
Physiological and Anatomical Responses of two Contrasting Pumpkin Genotypes Under Drought Stress
Mehmet Hamurcu¹, Canan Özdemir², Anamika Pandey¹, Mohd Khan¹, Zuhal Avsaroglu¹, Makbule Omay¹, Ismail Kaya¹, Erdogan Hakki¹, Sait Gezgin¹
¹Selcuk University, Konya, 420790, Turkey. ²Celal Bayar University, Manisa, 45140, Turkey
In this study, we investigated drought stress tolerance of pumpkin genotypes. PEG 6000 (6%) was applied to Hoagland nutrient solution to determine the effects of osmotic stress on drought tolerant and susceptible, C-26 genotype and C-27 genotypes, respectively. Different parameters including MDA content, H2O2 accumulation, OH sweeping activity, antioxidant enzymes like SOD, APX, CAT, POX, GR and GPX activities and anatomical structure of roots and leaves were examined. It was determined that under PEG 6000-induced drought stress, MDA content increased in both the experimental genotypes; however, greatest increase was observed in C-27 genotype. Moreover, H2O2 level and the OH radical sweeping activities of both pumpkin genotypes were increased under drought stress. However, both genotypes showed major differences in antioxidant enzyme activities under drought stress.
Confirmation of Significant Parent-of-Origin Effects in Cucumber
Madeline Olberg¹, Michael Havey²
¹University of Wisconsin, Madison, WI, USA. ²U.S. Department of Agriculture, Agricultural Research Service, Vegetable Crops Research Unit, Madison, WI, USA
Cucumber is a useful plant to study organellar effects on growth and development because chloroplasts are maternally and mitochondria paternally transmitted. Multiple doubled haploids (DH) were produced from four divergent cucumber populations, reciprocal crosses were made in a diallel mating scheme, and sizes of seeds and cotyledons and weights of plants approximately 25 days after planting were measured. General (GCA) and specific (SCA) combining abilities and reciprocal effects were highly significant. Fresh and dry weights were significantly different for specific reciprocal hybrids with identical nuclear genotypes, and revealing significant parent-of-origin effects. Reciprocal hybrids from crosses among multiple DHs extracted from the same cucumber cultivars were not consistent for early plant growth, indicating that parent-of-origin effects were specific to individual DHs and not to the population per se. These results further support reciprocal crossing of cucumber DHs and inbreds to identify the best performing hybrids.
Analysis of Physiological Characteristics and Chloroplast Ultrastructure of a New Leaf Color Mutant in Melon
Lai Yan¹,², Fu Qiushi¹, Lyu Jianchun¹, Zhou Mengdi¹, Huang Zhi², Wang Huaisong¹
¹Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China.
²College of Horticulture, Sichuan Agricultural University, Chengdu, China
The aim of the study was to study the differences in growth，physiological characteristics and chloroplast development between leaf color mutant (MT) and wild type (WT). Agronomic traits, photosynthetic parameters, photosynthetic pigment content, superoxide dismutase (SOD), peroxidase (POD), catalase (CAT) activity and MDA content and chloroplast ultrastructure of MT, WT, F1(MT×WT) and rF1(WT×MT) were investigated. The weaker growth of MT resulted in a delayed growth stage. There was no significant change in the photosynthetic rate. With hybridization F1, rF1 could go back to the normal growth. The leaf color of MT changed with the growth and developed from yellow to yellowish green, but the veins were still green. The chlorophyll content of MT leaf was significantly lower than that of WT. The Chlorophyll and carotenoid content were reduced by 25.69% and 21.26%, respectively, during the fruiting stage. However the ratio of chlorophyll a to chlorophyll b was significantly higher in the MT leaves than in WT leaves. SOD, POD and CAT enzyme activities and MDA content were higher in MT than in WT and then were increased by 65.45%, 13.91%, 3.23%, 15.14% in the stage, respectively. The observation of transmission electron microscopy (TEM) showed that the stacking of grana was irregular in the chloroplast structure of MT leaf and the grana lamellae were deranged with a line shape, indicating differences in the chloroplast structures between MT and WT. In the whole growth stage, the shorter height, lower chlorophyll content in WT than in MT and different chloroplast structure between them. There is no significant difference in photosynthetic rate, suggesting a basically intact function of photosynthetic apparatus. The antioxidant enzyme activity and was significantly higher in the MT than in the WT during fruiting stage and the MDA content was also significantly in the MT higher than in the WT during the whole growth stage. However, there was no significant difference among F1, rF1, and WT.
Introgression Mapping of Wild Species-Derived Resistance to Viruses in Cucurbita
Kyle LaPlant, Michael Mazourek
Cornell University, Ithaca, NY, USA
Viruses are major threats to global cucurbit production, capable of causing severe economic losses through plant stunting, reduced yield, and distortion of the fruit. Two of the most important viruses that are capable of infecting squash are papaya ringspot virus (PRSV) and cucumber mosaic virus (CMV). These viruses are transmitted by aphids in a non-persistent manner, making management of the diseases through vector difficult and ineffective. Breeding for resistance to these viruses is the most effective method of control; however, phenotypic selection for virus-resistant individuals by manual inoculation and inspection is laborious and slow. In addition, there are no identified sources of resistance to these viruses in Cucurbita pepo. Historically, virus resistance has been transferred to C. pepo from related species, such as Cucurbita ecuadorensis, and incorporated into the virus-resistant cultivars currently available. In order to elucidate the genes controlling these traits and improve breeding for virus resistance, we have evaluated the level of resistance to PRSV and CMV in a panel of C. pepo cultivars and historic Cornell breeding lines. These lines and C. ecuadorensis lines were genotyped using genotyping-by-sequencing. Using an introgression mapping approach, we have identified an approximately 2 MB introgression from C. ecuadorensis shared by the PRSV resistant lines. We are developing a mapping population with ‘Whitaker’, a cultivar resistant to PRSV and CMV, and ‘Success PM’, a susceptible cultivar. We will employ an F2:3 mapping approach to validate the PRSV resistance-associated region identified via introgression mapping and provide increased power for mapping CMV resistance. Mapping and validation efforts will lead to the development of markers for virus resistance loci and will be applied in marker- assisted selection.
Validation of KASPTM Assays for Three Alleles of a SUN gene Controlling Fruit Length and Shape in Watermelon (Citrullus lanatus)
Reeve Legendre, Cecilia McGregor
Department of Horticulture, University of Georgia, Athens, Georgia, USA
Fruit shape in watermelon (Citrullus lanatus) is a major concern for breeders and producers as it can influence consumer choice at point of sale in addition to impacting ease of shipping. Watermelon has a wide range of fruit shapes, but until recently, the genetic mechanisms underlying fruit length and shape have been unknown. While fruit phenotypes can be influenced by environmental factors, fruit length (FL) and shape (FSI) are believed to be controlled primarily by a SUN gene, Cla011257, located on chromosome 3 in a QTL associated with the traits. A 159-bp deletion (DEL) in a coding region, resulting in the absence of 53 amino acids, has been shown to be responsible for causing an elongated phenotype. We identified a new allele in Klondike Black Seeded (KBS) with a G to A point mutation in the third exon of Cla011257. KASPTM assays were developed for the three alleles of the gene and used to determine genotype-phenotype associations in five segregating populations. Phenotyping of three of the five populations and a diverse cultivar panel were grown in the field and phenotyped digitally with Tomato Analyzer (TA). TA phenotyping revealed relationships between the genotype and FL, fruit shape index (FSI), and the distal fruit end angle (DAN). The KASPTM assays for each allele of Cla011257 were significantly associated with three traits in the cultivar panel: FL (p-value < 0.0001), FSI (p-value < 0.0001), and DAN (p-value < 0.0001). Based on our results, the wild-type (WT) allele was associated with round fruit (FSI = 1.07 ± 0.02), and a wide distal end shape (152.25° ± 0.98°). The DEL allele, resulting from the 53 amino acid deletion, is associated with long fruit with the highest FSI (2.00 ± 0.02) with a narrow distal fruit end shape (98.55° ± 1.12°). The KBS allele is associated with an intermediate phenotype (FSI: 1.59 ± 0.02; DAN: 120.98° ± 1.24°). These KASPTM assays could be powerful tools in molecular watermelon breeding programs for marker assisted selection for fruit length and shape. Partial Funding provided by the Specialty Crop Block Grant Program at the U.S. Department of Agriculture (USDA) through Grant 14-SCBGP-CA-0006 (The CucCAP Project)
Molecular Mapping of a New Dominant Resistance Gene for Zucchini yellow mosaic virus (ZYMV) in Squash (Cucurbita pepo)
Haizhen Li, Guoyu Zhang, Fan Zhang, Jiaxing Tian
Beijing Vegetable Research Center, BAAFS, Beijing, China
Zucchini yellow mosaic virus (ZYMV) is one of the most destructive viruses that badly reduce the production of squash (Cucurbita pepo) all over the world. Resistance is the best approach to control the disease. Squash inbred line ‘BS12’ showed a high-level of ZYMV resistance in our germplasm evaluations over several years. The genetic basis of the resistance in ‘BS12’ was elucidated through an inheritance study and molecular mapping. A total of 1172 F2:3 lines from the crosses of BS3, a susceptible parent, with BS12 were tested with ZYMV-CH, a highly predominant ZYMV strain in China, under the controlled greenhouse conditions, and bulked segregant analysis was carried out to identify SSR and EST-SSR markers linked to this resistance gene. Results indicated that resistance to this virus observed in ‘BS12’ was controlled by a single dominant gene, and closely flanked by SSR markers ZY-140 and ZY-157 at a genetic distance of 0.4 and 2.6 cM, respectively. These markers were subsequently validated for detection of ZYMV resistance gene among 30 varieties: 10 squash genotypes were resistant to ZYMV, and 20 genotypes showed the susceptible banding pattern. The MAB strategy with these two markers enabled the development of homozygous (BC4F2) ZYMV-resistance lines with the smallest introgressed region and 96.9% of the recurrent parental genome, which proved valuable for ZYMV resistance gene transfer in future squash breeding.
Genetic Mapping Reveals Markers for Fruit Shape and Yellow Skin in Watermelon (Citrullus lanatus (Thunb.) Matsum. & Nakai)
Junling Dou, Xuqiang Lu, Aslam Ali, Shengjie Zhao, Nan He, Wenge Liu
Zhengzhou Fruit Research Institute, Zhengzhou, China
Watermelon has rich diversity in fruit shape and skin color, which are the major objectives of watermelon breeding. However, the candidate gene and the underlying genetic mechanism for such important trait in watermelon were unknown. In this study, we identified a locus on watermelon chromosome 3 controlling fruit shape and a locus on chromosome 4 for yellow skin. Segregation analysis in F2 and BC1 populations derived from a cross between two inbred lines ‘Duan125’ (elongate fruit) and ‘Zhengzhouzigua” (spherical fruit) suggested that fruit shape of watermelon was controlled by a single locus and elongate fruit (OO) was incompletely dominant to spherical fruit (oo) with the heterozygote (Oo) being oval fruit. A segregation analysis in F2 and BC1 populations derived from a cross of two inbred lines ‘94E1’(yellow skin) and ‘Qingfeng’(green skin) suggested that skin color is a qualitative trait. BSA-seq mapping in the F2 population showed the locus was located on chromosome 3, and the candidate gene was mapped to a region of 46 kb for fruit shape. There are only four genes present in the corresponding region in the reference genome. Sequencing of four candidate genes in this region showed that the CDS of Cla011257 had a 159 bp deletion, which resulted in the deletion of 53 amino acids in elongate watermelon. An indel marker was developed based on the deletion to test the F2 population and 105 watermelon germplasms. The results showed that Cla011257 cosegregated with watermelon fruit shape. BSA-seq mapping confirmed the locus for skin color in the F2 population, which was detected on chromosome 4 by GWAS among 330 varieties. Several major markers were designed to delimit the region to 59.8 kb region. Utilizing the two populations consisting of 10 yellow and 10 green skin watermelons, we found a tightly linked functional SNP marker for the yellow skin phenotype. The application of these markers as selection tool in breeding programs will help to improve the breeder’s ability to make selections at early stages of growth, thus accelerating the breeding program.
Chromosomal Locations of Four Loci Controlling Watermelon Seed Coat Color
Lucky Paudel, Josh Clevenger, Cecilia McGregor
University of Georgia, Athens, GA, USA
Global consumers associate watermelon with sweet, juicy fruits that are often consumed during the hot summer months. However, in some parts of Asia and Africa the lipid and protein rich watermelon seeds are the primary products from watermelon production. Seed coat color plays an important role in consumer preference for edible watermelon seeds and are therefore an important consideration during watermelon breeding. Watermelon seeds have diverse seed coat colors including black, stipple, red, green and white. A four gene model (R, T, W and D) was developed in the 1940s to explain the inheritance of these different phenotypes. In this study we re-examined the four gene model and identified the associated chromosomal loci. We utilized QTL-Seq and linkage mapping to map the four loci in three segregating F2 populations: Sugar Baby (stippled) x PI 482379 (green), Charleston Gray (stippled) x PI 189225 (red) and Charleston Gray (stipple) x UGA147 (clump). Our results confirmed that stipple (R_) is monogenically dominant over green (rr). The stipple x red population segregates for two genes, with the R gene being dominantly epistatic to the T gene. This epistatic interaction deviates from the expectation of the four gene model and we propose to name the latter locus T1. In the stipple x clump population, the D gene is recessively epistatic to W, as predicted by the model. The location of the R, T1, W and D loci were identified on chromosomes 3, 5, 6 and 8, respectively. KASPTM assays were developed for SNPs linked to the four loci and will facilitate maker assisted selection for watermelon seed coat color. Partial Funding provided by the Specialty Crop Block Grant Program at the U.S. Department of Agriculture (USDA) through Grant 14-SCBGP-CA-0006 (The CucCAP Project)
Increasing Shelf Life of Perishable Produce Using Patented Gene Technology
Venkatramana Pegadaraju, Jerry Feitelson
Agribody Technologies, San Diego, CA, USA
Post-Harvest Loss (PHL) in crops and food wastage pose major challenges to attaining sustainable standards for food security. Each year, 1.3 billion tonnes of food are globally wasted (FAO) representing a value close to $1 Trillion. Fruits and vegetables contribute to the highest rates of wastage. It’s estimated that every year about 45% of globally produced fruits and vegetables is wasted without consumption. Extending shelf-life of perishable produce is one of the mechanisms to minimize food wastage and increase food availability to feed the growing population. Agribody Technologies, Inc. (ATI) utilizes a combination of genome editing and a highly validated pair of conserved gene targets to significantly delay post-harvest senescence, while increasing resistance to abiotic (low nutrients, drought, heat, cold, salt, etc.) and biotic (fungal & bacterial) stresses, and increasing seed and biomass yield in crops. The efficacy of this technology has consistently been proven in multiple crops under both greenhouse and field conditions. Two years of replicated filed trial data in alfalfa have shown an unprecedent 20-45% yield increase in an elite commercial variety with no loss of quality. Similarly, field trials in banana and greenhouse studies in tomatoes and flowers have increased shelf-life by 2-to 3- fold. Currently, several licensing and co-development projects are underway in potatoes, coffee, canola and rice. Results from these studies will be discussed.
Development of Melon Cultivars for Organic Farming
Alejandro Flores¹, Alicia Sifres¹, Santiago García-Martínez², José Vicente Valcárcel¹, Gorka Perpiñá¹, Cristina Sáez¹, Carlos Romero³, Antonio Monforte³, Ana Pérez¹, Jaime Cebolla¹, María José Díez¹, Carmina Gisbert¹, Juan José Ruiz², Carmelo López¹, María Ferriol¹, Belén Picó¹
¹Universitat Politécnica de València, Valencia, Valencia, Spain. ²Universidad Miguel Hernández, Orihuela, Alicante, Spain. 3IBMCP (CSIC-UPV), Valencia, Valencia, Spain
Melon (Cucumis melo L.) has been cultivated in Spain since at least Roman times, both non- sweet melons (snake-shape, flexuosus type), locally known as alficós, and sweet melons. Snake melons were already cultivated in the first century, but the introduction of sweet melons from Central Asia probably occurred later, during the Middle Ages. Preferences of Spanish farmers and consumers during centuries favored the selection of varieties adapted to diverse agro- climatic conditions. Cultivars of six main groups of sweet melons, all belonging to the Inodorus group (non-climacteric, casaba types as Piel de Sapo, Rochet, Amarillo, Blanco, Tendral and Hilo Carrete) are still cultivated nowadays, although mainly for self-consumption or for local markets, with the exception of Piel de Sapo). Due to social demands of traditional fruits grown using organic farming practices, Valencian government (CEICE, Generalitat Valenciana) funded a project (PROMETEO2017/078) to select traditional Spanish melon cultivars appropriated for organic cultivation. Fifty cultivars representing the six classes of sweet melons and the non- sweet alficós were selected among those maintained at the Gene bank of the Polytechnic University of Valencia. Two experimental fields in the peri-urban area of Valencia, where organic farming is being recovered, were stablished. A survey of the main pests and diseases was conducted during the growing cycle. Aphid-transmitted viruses, such as Watermelon mosaic virus (WMV) and Cucumber mosaic virus (CMV) were the most frequent. Powdery mildew differentially affected the cultivars; Rochet and alficós cultivars were more tolerant than other types. In one of the fields, where melon had been cultivated for years, many soilborne fungal pathogens were isolated from plants showing different degrees of vine decline symptoms (Fusarium oxysporum, F. solani, Monosporascus cannonballus, and Macrophomina phaseolina); cultivars of Blanco and Amarillo types were more susceptible. Traditional melon varieties were grafted onto both Cucurbita and melon rootstocks, the latter tolerated better the soil fungi since F. solani affected the roots of the Cucurbita hybrids rootstocks. These assays allowed us to select the most tolerant cultivars and to identify the biotic factors limiting organic farming of melon in the region. This information would be used to optimize traditional melon breeding for organic cultivation.
lon Cultivars for Biosaline Agriculture
Santiago García-Martínez¹, Flores Alejandro², Alicia Sifres², José Vicente Valcárcel², Ana Pérez², Jaime Cebolla², Carmina Gisbert², María José Díez², Carmelo López², María Ferriol², Belén Picó², Juan José Ruiz¹
¹Universidad Miguel Hernández, Orihuela, Alicante, Spain. ²Universitat Politécnica de València, Valencia, Valencia, Spain
Salinity is an important factor limiting the productivity of crop plants. Biosaline agriculture deals with salinity, using unconventional saline water resources and crop breeding to support saline stress. Spain is the main melon producer and exporter in Europe. Modern improved hybrid cultivars are grown under conventional agriculture, but market is demanding diverse traditional cultivars, grown under sustainable systems. Low availability of fresh water is limiting this production. We have cultivated under saline conditions 20 melon cultivars in a field experiment conducted in an agricultural Wetland area included in the Carrizales Agrarian Natural Park (Southeast of Spain) (PROMETEO2017/078 funded by the Generalitat Valenciana). The climate is arid to semiarid Mediterranean (average annual rainfall of 250 mm). Drip irrigation was applied, using water with a conductivity ranging from 4 to 6 dS/m. Melon cultivars were grown ungrafted and grafted onto two rootstocks, an F1 Cucurbita hybrid and an F1 melon hybrid. Yield and fruit quality were compared with an assay grown in a field irrigated with non-saline water (1.9 dS/m). Adverse effects of saline irrigation were observed on plant growth only in some cultivars, mainly in ungrafted plants. As expected, plants grafted onto Cucurbita rootstocks were more vigorous. Most varieties yielded acceptable levels of high quality fruits, but differences in yield and fruit quality allowed the selection of those more appropriated for salt stress cultivation. Salinity slightly reduced yield, but no effect on mean fruit weight was observed (1.42 kg vs 1.41, for non-saline vs saline irrigation). Total soluble solids contents (SSC) increased under salt stress (11.9 vs 13.4). Rootstock effect on fruit size and quality was significant in saline conditions. Most cultivars gave higher yields and bigger fruits when grafted onto the Cucurbita rootstock (1.55 kg), whereas fruit size was similar in plants grafted onto melon rootstock and non-grafted plants (1.46 and 1.41 kg). The highest SSC were found using melon rootstocks (13.6) compared to the Cucurbita and the non-grafted (13.3 and 13.1). The selection of the best traditional cultivars and best scion-rootstock combinations will enhance the implementation of biosaline agriculture in melon crop.
Selection of Traditional Spanish MeStudy of Hybridity in Cucumber (Cucumis sativus L.) Under Polyhouse Condition
Dinesh Singh, Tusar Sahoo
G.B. Pant University of Agriculture & Technology, Pantnagar ,Udham Singh Nagar, Uttrakhand, India
Present investigation was carried out at vegetable research centre and NAIP Lab, Department of vegetable science, G.B.P.U.A & T., Pantnagar, Uttarakhand during August 2015 to December 2016. The main objectives to study the hybridity among monoecious, gynoecious and parthenocarpic genetic background in cucumber (Cucumis sativus L.). Most of the genotypes were early to medium in flowering. Maximum values with respect to number of fruits per plant (19.00), fruit length (22.36 cm), average fruit weight (270.33 g) were found in PCUCP-4 x PCUC- 8, PCUCP-3 and PCUCP-3 x PCUC-25, respectively under environment 2 (E2). Fruit yield (q/ha) varied from 105.24 to 1367 and E2 yield was higher than environment 1 (E1). The parthenocarpic lines and gynoecious lines exhibited superior performance in E2 as compared to E1 as environment differences influence the yield and yield contributing characters. Across the environments, PCUCP-4 x PCUC-8 and PCUCP-5 x PCUC-8 genotypes were found promising for heterobeltiosis and standard heterosis over check. PCUCP-4 x PCUC-8 and PGYG-3 x PCUC-25 showed significant specific combining ability for the maximum traits in both environments. Therefore, it is concluded that F1 hybrids PCUCP-4 x PCUC-8, PCUCP-3 x PCUC-25, PCUCP-3 x Pant Khira-1, PCUCP-5 x PCUC-8 and PGYG-3 x PCUC-25 can be exploited for commercial cultivation under protected cultivation. Genotypes PCUCP-4, PCUCP-3 and PCUCP-1 were found the best general combiner and tester PCUC-8 found the overall best general combiner in both the environments. Among genotypes PCUCP-5 and PGYC-2 were fond the most diverse and PCUCP-4 and PCUCP-8 found most closely related with each other. Among markers, UBC-834 and UBC-840 can be used for further identification purpose as these have possessed highest PIC value and polymorphism. ISSR analysis amplified a total of 69 loci with 75-100% polymorphism. Use of ISSR markers will certainly help to identify genetic diversity, management and exploration of the genetic resources and assist in the genetic improvement of cucumber.
Genetic Characterization of DH-Kirkagac Melon Lines Revealed by SSR Markers
Baris Dal, Nebahat Sari, Yildiz Aka Kacar, Ilknur Solmaz
Çukurova University, Adana, Turkey
Melon is an economically important vegetable crop in Turkey. The production amount is approximately 1.7 million tonnes and winter type melons (Cucumis melo L. var. inodorus) are widely grown in many regions using local genotypes. Haploidization technique is known to be a useful tool in plant breeding by reducing time for the production of 100% homozygous lines. We examined the genetic relationships of 96 DH-Kirkagac melon genotypes that we developed by irradiated pollen technique using SSR (Simple Sequence Repeat) markers. Twenty polymorphic SSR markers were used and based on SSR data, the genetic similarity coefficients were calculated and dendrograms were constructed using UPGMA (unweighted pair-group method with arithmetic average). According to cluster analysis DH-lines were separated into different groups. Our results provide us different heterotic groups for developing new breeding programmes in Kirkagac melons.
QTL Mapping of Angular Leaf Spot Resistance in Cucumber
Junyi Tan¹, Zhiming Wu², Yuhui Wang¹, Yiqun Weng³
¹Horticulture Department, University of Wisconsin-Madison, Madison, WI, USA. ²Institute of Cash Crops, Hebei Academy of Agriculture & Forestry Sciences, Shijiazhuang, Hebei, China. 3U.S. Department of Agriculture, Agricultural Research Service, Vegetable Crops Research Unit, Madison, WI, USA
Angular leaf spot (ALS) is an important disease of cucumber worldwide. The causal agent for ALS is the bacterial Pseudomonas syringae pv. lachrymans. Here, we reported quantitative trait locus (QTL) mapping and cloning of a resistance gene to a virulent strain of the ALS pathogen in two cucumber inbred lines Gy14 and WI 2757 with 129 recombinant inbred lines (RILs from the cross of Gy14 x 9930 (G9RIL) and 132 F2:3 families from the crosses between WI 2757 and True Lemon (WTF23). Phenotyping of angular leaf spot inoculation responses were conducted in five controlled environments (CA2011, WI2011, WI2015, WI2016, WI2017). QTL analysis suggested that the major- effect psl locus for ALS resistance on Chromosome 5 was carried by Gy14 and WI2757. One additional minor-effect QTL psl1.1 was only detected in WI2011 environment and another minor-effect QTL psl3.1 was only detected in CA2011 environment in the WTF23 population. Additional 375 G9RILs were employed for fine mapping of the psl locus, which allowed to delimit the resistance locus into a 93.7-kb region in which 12 genes were predicted including the cucumber staygreen (CsSGR) gene that is known to play a critical regulatory role in the chlorophyll degradation pathway. Local association analysis among 82 lines of the natural cucumber population with 623 SNPs provided further evidence that CsSGR is the candidate gene for ALS resistance QTL (psl). A single nucleotide mutation in the coding region of CsSGR resulted in a nonsynonymous amino acid substitution in SGR protein, which is predicted to be responsible for the differential inoculation responses against the ALS pathogen infection between Gy14 and 9930. From qPCR, CsSGR was significantly upregulated upon pathogen inoculation in the susceptible 9930 as compared to the resistant Gy14. Genes involved in the chlorophyll degradation pathway exhibited differential expression between resistant and susceptible lines post pathogen inoculation. This work will help us further reveal host disease resistance mediated by a loss-of- susceptibility mutation of CsSGR. National Institute of Food and Agriculture, U.S. Department of Agriculture, under award numbers 2011-51181-30661 and 2015-51181-24285. Partial Funding provided by the Specialty Crop Block Grant Program at the U.S. Department of Agriculture (USDA) through Grant 14-SCBGP-CA-0006 (The CucCAP Project)
Physiological Responses of Melon Genotypes with Known Drought Tolerance Levels
Ayse Torun¹, Mehmet Hamurcu¹, Nebahat Sarı²
¹Selcuk University, Konya, Turkey. ²Çukurova University, Adana, Turkey
If available agricultural land in the world would be classified according to stress factors, then drought stress is one of the most common environmental stresses, affecting 26% of plant’s growth and efficiency. Identification of plant species and genotypes that are resistant to drought stress, and development of varieties that are differentially tolerant to drought stress is one of the crucial priorities in agricultural sciences. The most important biochemical change in plants under drought stress is, formation of reactive oxygen compounds such as single oxygen, superoxide anion and hydrogen peroxide due to a decrease in photosynthesis rate. Reactive oxygen compounds accumulating under stress conditions are natural by-products of cell metabolism and play an important role in signal transduction mechanism. However, in case of excessive accumulation, they can lead to cell death by inducing lipid peroxidation, protein reduction and DNA fragmentation. Plants utilize enzymatic or non-enzymatic antioxidant molecules to deal with the oxidative stress caused by accumulation of reactive oxygen compounds. In this study, Kav-248 (drought tolerant) and Kav-20 (drought sensitive) genotypes were used, which were selected among 192 Turkish melon germplasms with two different screenings, were conducted in climate controlled greenhouses and climate chambers to determine drought tolerance levels. In the environment where melon genotypes were exposed to PEG 6000-induced drought stress, the defense mechanisms exhibited by the plants were compared with control groups. Antioxidant enzymes (SOD, POX, GR and CAT), known as internal defense systems of genotypes against drought stress and changes in reactive oxygen species were examined. While the SOD activity increased by 86% in Kav-248 genotype tolerant to dry conditions compared to control, it is increased by 75% in Kav-20 genotype sensitive to dry conditions compared to control. GR activity increased by 37% in Kav-248 genotype compared to control, while Kav-20 genotype increased by 10%. OH radical sweeping activities increased by 150% in the Kav-248 genotype, while increased by 181% in the Kav-20 genotype, and similarly, increased H2O2 radically due to drought application and the maximum increase in the Kav-20 genotype according to the control were determined.
Next-Generation Sequencing Bulk Segregant Analysis Reveals Multiple Loci Involved in Phytophthora Root and Crown Rot in Squash and Pumpkin
Gregory Vogel¹,², Kyle LaPlant¹, Michael Mazourek¹, Michael Gore¹, Christine Smart²
¹Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA. ²Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Geneva, NY, USA
Breeding for resistance to the various disease syndromes caused by the oomycete pathogen Phytophthora capsici has been challenging in Cucurbitaceae species. Few sources of resistance have been identified and evidence to date suggests that different genes play a role in resistance in distinct plant parts. Despite these difficulties, progress can be made in selection for quantitative resistance to specific disease syndromes. Our work is focused on squash and pumpkin (Cucurbita pepo), which are particularly susceptible to Phytophthora root and crown rot. Using white vegetable marrow landrace ‘Austrian Bush’ as the primary source of resistance, we have developed breeding lines that display reduced root and crown rot symptoms after inoculation with P. capsici. In order to elucidate the genetic basis of the trait and discover molecular markers for use in breeding, we performed QTL mapping using a next-generation sequencing bulk segregant analysis (NGS-BSA) approach. Over 13,000 F2 individuals from a cross between susceptible zucchini cultivar ‘Dunja’ and a partially resistant breeding line were inoculated as seedlings in the greenhouse with a zoospore suspension of P. capsici. Pools consisting of the 15% most susceptible and resistant individuals, in addition to a control pool of random individuals, were visually selected in each of two biological replicates. DNA samples from each pool were then whole-genome resequenced. Allele counts at over 150,000 single- nucleotide polymorphisms were used to identify genomic regions where allele frequencies differed between control, susceptible, and resistant pools. Results suggest polygenic inheritance, and beneficial alleles originating from both the susceptible and partially resistant parents. We failed to observe any region with more than a 15% difference in allele frequency between susceptible and resistant pools, indicating small QTL effect sizes or poor accuracy in visual selection due to low single-plant heritability. Segments on chromosomes 4, 5, 8, and 16 displayed the most extreme allele frequency differences between pools. The effects of DNA polymorphisms located in these regions will be validated in additional populations in order to evaluate their usefulness in genomics-assisted selection.
QTL Mapping of Resistance to Powdery Mildew in Cucumis melo MR-1 Using a Recombinant Inbred Line Population
Sandra Branham, W. Patrick Wechter, Mahir Mandal, Jennifer Ikerd, Shaker Kousik
U.S. Department of Agriculture, Agricultural Research Service, U.S. Vegetable Laboratory, Charleston, SC, USA
One hundred seventy-two lines of an MR-1 x AY RIL population (F6 to F11) were evaluated for resistance to cucurbit powdery mildew incited by Podosphaera xanthii race 1 (Px race 1) in greenhouse trials. The RIL population was evaluated in two independent greenhouse tests in April 2016 and February 2017 using a 0-10 scale of increasing disease severity. Disease severity scores across the population were heavily skewed towards resistance for all tissue types but were still continuous as the distributions all extended to a score of at least 5. Population disease severity means varied from 0.67 for the stem to 2.6 for rating of true leaves. There was no evidence for transgressive segregation. We identified two major QTL (qPx1-5 and qPx1-12), two minor QTL (qPx1-4 and qPx1-10), and one epistatic interaction associated with disease severity BLUPs of the true leaves. The same four QTL, or a subset thereof, defined by overlapping 1.5-LOD intervals were identified for all tissue types. The two major QTL alone (qPx1-5 and qPx1-12) explained more than 74% of the variation in disease severity and had LOD scores of 46.1 and 36.6, respectively. MR-1 contributed the resistance alleles for all QTL. A significant epistatic interaction between qPx1-5 and qPx1-12 was detected, in which the resistance allele of qPx1-5 masks the effect of the susceptible allele of qPx1-12. Partial Funding provided by the Specialty Crop Block Grant Program at the U.S. Department of Agriculture (USDA) through Grant 14-SCBGP-CA-0006 (The CucCAP Project)
Genomics-Assisted Molecular Breeding in Watermelon
Shaogui Guo¹,², Xin Wang², Honghe Sun¹, Shengjie Zhao3, Shan Wu², Yi Ren¹, Jie Zhang1, Guoyi Gong¹, Haiying Zhang¹, Wenge Liu³, Zhangjun Fei², Yong Xu¹
¹Beijing Vegetable Research Center of Beijing Academy of Agriculture and Forestry Sciences, Beijing, China. ²Boyce Thompson Institute, Ithaca, NY, USA. ³Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
Watermelon is one of the most popular fruit crops worldwide. Accumulative genome and transcriptome resources have provided a solid foundation to help elucidate molecular mechanisms underlying horticultural traits and identify genes and molecular markers that can be used to facilitate watermelon breeding. To meet the increasing demands for watermelon varieties with improved flavor, nutrient composition and appearance, we have identified and characterized genes regulating fruit flesh sweetness and flesh color. We have also identified the genetic components that control watermelon sex determination. This knowledge has been applied to the generation of gynoecious varieties in order to increase the fruit yield and the efficiency of seed production. We have identified sources of resistance to Fusarium wilt, powdery mildew and Zucchini yellow mosaic virus (ZYMV) from the wild and semi-wild watermelon germplasms, which have been used in watermelon disease resistance breeding. In addition, we have performed genome-wide association studies (GWAS) on these fruit quality and disease resistance traits and identified a number of highly associated DNA markers. To increase the efficiency of watermelon improvement by taking advantage of genomics-assisted breeding, we have set up an ultra-high-throughput genotyping platform. Furthermore, we have successfully implemented the CRISPR/Cas9 gene editing technology in watermelon and used this technology to generate the world first tribenuron herbicide-resistant watermelon line.
A High-Density Genetic Map Construction and Identifying QTLs Associated with Fruit Shape in Pumpkin (Cucurbita moschata Duchesne)
Guoyu Zhang, Haizhen Li, Fan Zhang, Jiaxing Tian
Beijing vegetable research center, Beijing, China
Pumpkin (Cucurbita moschata Duch.) is an economically important crop belonging to the Cucurbitaceae family. However very few genomic and genetic resources are available for this species. A high-density genetic map can facilitate quantitative trait loci (QTL) mapping. A set of 186 F2 progenies derived from the cross of pumpkin inbred lines Rifu and Honey jujube were genotyped using the genotyping-by-sequencing approach. Using the SNPs we identified, a high- density genetic map containing 656 bin-markers was constructed, spanning a total genetic distance of 3136.90 cM across the 20 linkage groups of C. moschata with a mean marker density of 4.78 cM. The high-density genetic map was used to identify genomic regions highly associated with an important agronomic trait, fruit shape index. Three QTLs on linkage groups (LGs) 2, 6 and 16, respectively, were recovered. One QTL, qCoFs, which was located in an interval of 0.15 Mb on LG 2 containing 36 putative genes, explained 55.7 phenotypic variations. The map provided a valuable resource for gene cloning and marker assisted breeding in pumpkin. The identified fruit shape index QTLs would help to further mapping the genes and dissect the underlying molecular basis regulating pumpkin fruit shape development.
Target SSR-seq: A New SSR Genotyping Technology and its Application In Genetic Analysis and Cultivar identification in Cucumis sativus L.
Jingjing Yang¹, Jian Zhang¹, Zhonghua Zhang², Han Miao², Yong Xu¹, Changlong Wen¹
¹Beijing Vegetable Research Center, Beijing Academy of Agricultural and Forestry Sciences, Beijing, China. ²Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
Abstract: Simple sequence repeats (SSR) or microsatellites, as the second generation of molecular markers, have been extensively used in many research areas. However, the existing SSR exploitation and detection techniques cannot efficiently and accurately acquire hundreds of SSR genotypes. We designed a new technology called Target SSR-seq which combined the advantages of high throughput sequencing and multiplex amplification of SSR regions. It could automatically gain hundreds of SSR genotypes at once by sequencing the SSR motif at the coverage of 1000 times by HighSeq sequencing platform. The application of target SSR-seq in the present study was to establish 382 cucumber cultivar fingerprint database using 111 perfect SSR through analyzing 182 cucumber resources re-sequencing data. A total of 398 alleles within 111 perfect SSR loci were acquired and the average sequencing depths of all cultivars were 1289X. Population analysis showed that 382 cucumber cultivars were divided into four populations: “North China type,” “South China type,” “Europe fruit type” and “Xishuangbanna type.” The genetic relationship matrix among 382 cucumber cultivars was constructed based on the number of different SSR markers. We found “Jingyouyihao” has higher genetic similarity while fruit cucumber cultivars had further genetic distance with other cultivars. Consequently, 16 core SSR pairs were able to accurately distinguished 382 cucumber varieties, which demonstrated that target SSR-seq had high accurate and efficiency for SSR genotyping and especially suit for DNA fingerprinting research.