[Show abstract][Hide abstract] ABSTRACT: Our genetic diversity study uses microsatellites of known map position to estimate genome level population structure and linkage disequilibrium, and to identify genomic regions that have undergone selection during watermelon domestication and improvement. Thirty regions that showed evidence of selective sweep were scanned for the presence of candidate genes using the watermelon genome browser (www.icugi.org). We localized selective sweeps in intergenic regions, close to the promoters, and within the exons and introns of various genes. This study provided an evidence of convergent evolution for the presence of diverse ecotypes with special reference to American and European ecotypes. Our search for location of linked markers in the whole-genome draft sequence revealed that BVWS00358, a GA repeat microsatellite, is the GAGA type transcription factor located in the 5′ untranslated regions of a structure and insertion element that expresses a Cys2His2 Zinc finger motif, with presumed biological processes related to chitin response and transcriptional regulation. In addition, BVWS01708, an ATT repeat microsatellite, located in the promoter of a DTW domain-containing protein (Cla002761); and 2 other simple sequence repeats that association mapping link to fruit length and rind thickness.
The Journal of heredity 11/2014; · 1.97 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: We used genotyping by sequencing to identify a set of 10,480 single nucleotide polymorphism (SNP) markers for constructing a high-resolution genetic map of 1,096 cM for watermelon. We assessed the genome-wide variation in recombination rate (GWRR) across the map and found an association between GWRR and genome-wide nucleotide diversity. Colinearity between the map and the genome-wide reference sequence for watermelon was studied to identify inconsistency and chromosome rearrangements. We assessed genome-wide nucleotide diversity, linkage disequilibrium (LD) and selective sweep for wild, semi-wild and domesticated accessions of Citrullus lanatus var. lanatus to track signals of domestication. Principal component analysis combined with chromosome-wide phylogenetic study based on 1,563 SNPs obtained after LD pruning with minor allele frequency = 0.05 resolved the differences between semi-wild and wild accessions as well as relationships among worldwide sweet watermelon. Population structure analysis revealed predominant ancestries for wild, semi-wild and domesticated watermelons as well as admixture of various ancestries that were important for domestication. Sliding window analysis of Tajima's D across various chromosomes was used to resolve selective sweep. LD decay was estimated for various chromosomes. We identified a strong selective sweep on chromosome 3 consisting of important genes that might have had a role in sweet watermelon domestication.
[Show abstract][Hide abstract] ABSTRACT: Background
A large single nucleotide polymorphism (SNP) dataset was used to analyze genome-wide diversity in a diverse collection of watermelon cultivars representing globally cultivated, watermelon genetic diversity. The marker density required for conducting successful association mapping depends on the extent of linkage disequilibrium (LD) within a population. Use of genotyping by sequencing reveals large numbers of SNPs that in turn generate opportunities in genome-wide association mapping and marker-assisted selection, even in crops such as watermelon for which few genomic resources are available. In this paper, we used genome-wide genetic diversity to study LD, selective sweeps, and pairwise FST distributions among worldwide cultivated watermelons to track signals of domestication.
We examined 183 Citrullus lanatus var. lanatus accessions representing domesticated watermelon and generated a set of 11,485 SNP markers using genotyping by sequencing. With a diverse panel of worldwide cultivated watermelons, we identified a set of 5,254 SNPs with a minor allele frequency of >= 0.05, distributed across the genome. All ancestries were traced to Africa and an admixture of various ancestries constituted secondary gene pools across various continents. A sliding window analysis using pairwise FST values was used to resolve selective sweeps. We identified strong selection on chromosomes 3 and 9 that might have contributed to the domestication process. Pairwise analysis of adjacent SNPs within a chromosome as well as within a haplotype allowed us to estimate genome-wide LD decay. LD was also detected within individual genes on various chromosomes. Principal component and ancestry analyses were used to account for population structure in a genome-wide association study. We further mapped important genes for soluble solid content using a mixed linear model.
Information concerning the SNP resources, population structure, and LD developed in this study will help in identifying agronomically important candidate genes from the genomic regions underlying selection and for mapping quantitative trait loci using a genome-wide association study in sweet watermelon.
[Show abstract][Hide abstract] ABSTRACT: Cucurbit bacterial fruit blotch caused by Acidovorax avenue subsp. citrulli is a significant threat to watermelon [Citrullus lanatus (Thunb.) Matsum. and Nakai] production worldwide. The disease can cause complete loss of marketable crop under ideal conditions. Since seed is the primary inoculum for bacterial fruit blotch in cucurbit crops, bacteria-free seed production has helped limiting outbreaks. Currently, the most effective strategy for managing bacterial fruit blotch has been excluding the pathogen from seeds, fruits, and transplants. However, efficacy of the external treatments varies because bacteria can be under the seed coat. Therefore, genetic resistance would be of great scientific and economic value. The overall objective of this study was to identify resistance to bacterial fruit blotch using the available Plant Introductions accessions in the USDA germplasm collection. Field evaluations based on foliar disease symptoms at the adult stage were conducted at Clinton, NC, in Summer 2011 to 2013. The experiment was a randomized complete block with 1689 cultigens, 3 years, and 2 replications of single-plant plots. Selected PIs were tested at the two-true leaf stage in a controlled environment in 2013 to confirm the resistance source. Studies are under way to improve the disease rating system by accounting for different growth stage and leaf type. Both field and greenhouse screening adopted a rating scale with 0–9 (0 = no symptoms, 1–2 = trace, 3–4 = slight, 5–6 = moderate, 7–8 = severe, and 9 = dead). Statistical analysis on weekly ratings showed that significant differences exist in disease severity among accessions (P = 0.05). The 10 most resistant and 2 most susceptible accessions were identified and then confirmed in retest experiments. Resistant germplasm will be made available for those interested in developing molecular markers and improved cultivars.
[Show abstract][Hide abstract] ABSTRACT: Bitterness in cucumber fruit and foliage is due to the presence of cucurbitacins. Several genes have been described that control the trait, with bi (bi-1) making fruit and foliage bitter free and Bt (Bt-1) making the fruit highly bitter. Previous studies have reported the inheritance and molecular markers linked to bi-1 or Bt-1, but we were interested in studying the inheritance of fruit bitterness in the progeny of 2 nonbitter fruit inbred lines. The objective was to determine the inheritance of cucumber fruit and foliage bitterness and to locate them on a current linkage map using a recombinant inbred lines (RILs) population derived by crossing 9110Gt and 9930. It was concluded from the inheritance analysis that there were 2 loci controlling fruit bitterness in the population. One locus was in the same position as the location previously identified for bi-1, and another locus was for bi-3. Using a simple sequence repeat (SSR) linkage map, 2 loci for fruit bitterness in this RILs population were mapped. The locus of bi-1 was located at the region between SSR0004 and SSR02309 within the genetic distance of 5.2 cM on chromosome 6. The locus of bi-3 was placed in the region of SSR00116-SSR05321 within the genetic distance of 6.3 cM on chromosome 5. The physical distances for the regions of bi-1 and bi-3 were 11,430.94 Kb with 160 predicted genes and 1528.23 Kb with 198 predicted genes, respectively. Among 160 predicted genes for bi-1, there is a terpene synthase gene named Csa008595, which was speculated as the candidate gene of bi-1.
The Journal of heredity 10/2012; · 1.97 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Cucurbits are a group of diverse horticultural species grown worldwide. Their fruit are consumed fresh, cooked, or processed, and seeds can be eaten or used for their high quality cooking oil and protein meal. India and Southeast Asia, including China, comprise the primary and secondary centers of diversity, respectively, of cucumber (Cucumis sativus L.). India and central and southwest Asia comprise the primary center of diversity for melon (Cucumis melo L.), with China as a secondary center. Watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai var. lanatus] is important throughout Asia, although its primary center of diversity is west and central Africa. European forms of melon, cucumber and watermelon were introduced to the New World multiple times. Asian varieties of these and other cucurbits [e.g., bitter (Momordica charantia L.) and luffa (Luffa cylindrical L.) gourds] have been introduced to the U.S from the late 1800s to the present. Sustainability and improvement of U.S. melon, cucumber, and watermelon varieties have been achieved through introgression of genes from their respective Asian germplasm pools for disease and pest resistance, increased genetic diversity, productivity, and quality. Resistance to Podosphaera xanthii (Castagne) Braun & Shishkoff was first found in two Indian melons. Three types of resistance to melon aphid (Aphis gossypii Glover) were found in melons from India and Korea. Cucumis hystrix from China was crossed with cucumber to create the amphidiploid (Cucumis hytivusChen and Kirkbride) through which novel genetic variation was introgressed to cucumber. Gynoecious sex expression in cucumber was derived from Japan. Asian watermelon accessions may be the source for canary yellow flesh, which adds unique nutritional and flavor content to our diet. Technological advancement and genetic improvement pioneered in Asia advanced cucurbit production worldwide. Research on the feasibility of seedless watermelon was initiated in Japan in the late 1920s. Today, seedless types account for a major share of the watermelon market. Grafting, which originated in Asia in 1920s, using disease- and pest-resistant, or cold tolerant rootstocks is essential for sustainable cucurbit production in many parts of the world, and holds great potential as an alternative to methyl bromide fumigation. For example, interspecific hybrids of Cucurbita maxima Duch. and Cucurbita moschata Duch. ex Poir., two New World species, are the most widely used rootstock for cucurbits in Japan and South Korea, and Indian bottle gourd (Lagenaria siceraria L.) introductions of Indian origin are valuable sources of germplasm for breeding multiple disease resistant rootstocks.
[Show abstract][Hide abstract] ABSTRACT: Elite cultivars of watermelon (Citrullus lanatus (Thunb.) Matsum. & Nakai) are high in fruit quality but may not be the highest yielders. The objective of this study was to estimate the heritability of, and genotypic and phenotypic correlations among, yield traits in two watermelon populations developed from crosses between obsolete cultivars with high yield and elite modern cultivars. Field trials were conducted at two locations in North Carolina (Clinton and Kinston). The data were analyzed by regressing S0:1 progeny data on S0 parent data to estimate narrow-sense heritability. Narrow-sense heritability estimates were low for all traits measured [total fruit weight (0.04–0.12), marketable fruit weight (0.06–0.15), total fruit number (0.04–0.16), fruit size (0.18–0.19), and percent culls (0.02–0.09) in North Carolina Watermelon 1 (NCWP1) and North Carolina Watermelon 2 (NCWP2) populations, respectively]. Estimates of broad-sense heritability were higher than estimates of narrow-sense heritability. Total fruit weight and marketable fruit weight were highly correlated (r
g = 0.97–1.00). Marketable fruit weight and fruit size used as single selection criteria in NCWP1 and total fruit number in NCWP2, were predicted to give the best correlated response for total fruit weight. Narrow-sense heritability was low for fruit yield; therefore, watermelon breeders should select based on replicated progeny rows in multiple environments to maximize gain.
[Show abstract][Hide abstract] ABSTRACT: The watermelon (Citrullus lanatus (Thunb.) Matsum. & Nakai var. lanatus) has high variability for fruit size, shape, rind pattern, and flesh color. This study was designed to measure the qualitative inheritance of rind phenotypes (solid dark green vs. light green). For each of the 2 families, "Mountain Hoosier" × "Minilee" and "Early Arizona" × "Minilee," 6 generations (P(a)S(1), P(b)S(1), F(1), F(2), BC(1)P(a), BC(1)P(b)) were developed. Each family was tested in summer 2008 in 3 environments in North Carolina. Phenotypic data were analyzed with the χ(2) method to test the segregation of Mendelian genes. Deviations from the expected segregation ratios based on hypothesized single dominant gene for solid dark green versus light green rind pattern were recorded, raising questions on the inheritance of this trait. Inheritance of solid dark green rind versus light (gray) rind showed duplicate dominant epistasis. Duplicate dominant epistasis gives rise to a 15:1 ratio (solid dark green:light rind pattern) in F(2) generation. When both the loci are homozygous recessive, we observe light rind pattern. The g-1 and g-2 genes were identified to control light green rind when in homozygous recessive form.
The Journal of heredity 06/2011; 102(4):489-93. · 1.97 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Breeding for high phytonutrient fruits and vegetables can be a fairly straightforward endeavor when the compounds of interest produce a visible effect or the methods for quantifying the compounds simple and inexpensive. Lycopene in tomatoes and watermelon is one such compound, since the amount of red corresponds well with the quantity of lycopene produced. Because of this, breeders have developed high lycopene varieties. High antioxidant concentration in these vegetables creates new marketing tools for improved sales, premium price options, and nutrient packed product. Unfortunately, testing for many health promoting compounds is labor intensive and expensive. For this reason, these compounds are usually not quantified or selected for in breeding lines. Preliminary experiments on watermelon breeding lines showed a wide range in the amount of citrulline (6 fold differences between high and low) and the tripeptide antioxidant glutathione (24 fold differences) expressed within open pollinated varieties. This divergent expression of health promoting amino acids and peptides makes it difficult for industry groups to make blanket health claims for individual crops. By using new strategies and methods, it is becoming easier to test for many of these compounds to insure nutrient packed produce for the market place. Our finding on citrulline and glutathione demonstrate the feasibility of new analytical technology to develop breeding strategies for developing more nutritive produce.
[Show abstract][Hide abstract] ABSTRACT: Powdery mildew caused by Podosphaera xanthii has recently become an important disease of watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai] in the United States. The disease can be controlled with fungicides, but it would be more economical and environmentally safe to use genetic resistance. Here, we report sources of resistance to powdery mildew race 2W identified in the evaluation of the entire U.S. watermelon Plant Introduction collection made of four Citrullus Schrad. ex. Eckl. & Zeyh. species and Praecitrullus fistulosus (Stocks) Pangalo species. A total of 1654 PI accessions, cultivars, and breeding lines (hereafter collectively referred to as cultigens) were tested in the greenhouse using at least seven replications. From that, 54 cultigens including the 44 most resistant and 10 susceptible checks were retested in greenhouse and field experiments. All cultigens showed symptoms of powdery mildew. Resistance was identified in wild PI accessions. Eight cultigens had high resistance and 21 had intermediate resistance. Leaf and stem disease severity ratings were positively correlated (r = 0.86, P < 0.0001). Data were summarized from the screening and retest studies, and the most resistant cultigens were PI 632755, PI 386015, PI 189225, PI 346082, PI 525082, PI 432337, PI 386024, and PI 269365. The most susceptible cultigens were PI 222775 and PI 269677. Many of the resistant cultigens originated from Nigeria and Zimbabwe.
[Show abstract][Hide abstract] ABSTRACT: Zucchini yellow mosaic virus (ZYMV) is one of the most economically important potyviruses infecting cucurbit crops worldwide. Using a candidate gene approach, we cloned and sequenced eIF4E and eIF(iso)4E gene segments in watermelon. Analysis of the nucleotide sequences between the ZYMV-resistant watermelon plant introduction PI 595203 (Citrullus lanatus var. lanatus) and the ZYMV-susceptible watermelon cultivar 'New Hampshire Midget' ('NHM') showed the presence of single nucleotide polymorphisms (SNPs). Initial analysis of the identified SNPs in association studies indicated that SNPs in the eIF4E, but not eIF(iso)4E, were closely associated to the phenotype of ZYMV-resistance in 70 F(2) and 114 BC(1R) progenies. Subsequently, we focused our efforts in obtaining the entire genomic sequence of watermelon eIF4E. Three SNPs were identified between PI 595203 and NHM. One of the SNPs (A241C) was in exon 1 and the other two SNPs (C309A and T554G) were in the first intron of the gene. SNP241 which resulted in an amino acid substitution (proline to threonine) was shown to be located in the critical cap recognition and binding area, similar to that of several plant species resistance to potyviruses. Analysis of a cleaved amplified polymorphism sequence (CAPS) marker derived from this SNP in F(2) and BC(1R) populations demonstrated a cosegregation between the CAPS-2 marker and their ZYMV resistance or susceptibility phenotype. When we investigated whether such SNP mutation in the eIF4E was also conserved in several other PIs of C. lanatus var. citroides, we identified a different SNP (A171G) resulting in another amino acid substitution (D71G) from four ZYMV-resistant C. lanatus var. citroides (PI 244018, PI 482261, PI 482299, and PI 482322). Additional CAPS markers were also identified. Availability of all these CAPS markers will enable marker-aided breeding of watermelon for ZYMV resistance.
Theoretical and Applied Genetics 10/2009; 120(1):191-200. · 3.51 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: ADDITIONAL INDEX WORDS. cold tolerance, Cucumis sativus, vegetable breeding ABSTRACT. An experiment was conducted to determine the genetics of chilling resistance in cucumber (Cucumis sativus L.) inbred NC-76 that was developed from PI 246930, an accession from the U.S. Department of Agriculture germplasm collection. NC-76 was crossed with 'Chipper' and breeding line Gy 14 to produce F1 ,F 1 reciprocal, F2, and BC1 generations for evaluation. Cucumber seedlings at the first true leaf stage were placed in growth chambers set at 4 8C for 7 h and a photosynthetic photon flux of 500 mmolm-2s-1. Segregation in the F2 fit a 3 : 1 inheritance pattern, with resistance being dominant. The backcross of the F1 to the susceptible parent produced a 1 : 1 ratio, confirming that chilling resistance was from a single gene. The single dominant gene controlling chilling resistance in NC-76 was given the symbol Ch.
[Show abstract][Hide abstract] ABSTRACT: Plant breeders are interested in the analysis of phenotypic data to measure genetic effects and heritability of quantitative traits and predict gain from selection. Measurement of phenotypic values of 6 related generations (parents, F(1), F(2), and backcrosses) allows for the simultaneous analysis of both Mendelian and quantitative traits. In 1997, Liu et al. released a SAS software based program (SASGENE) for the analysis of inheritance and linkage of qualitative traits. We have developed a new program (SASQuant) that estimates gene effects (Hayman's model), genetic variances, heritability, predicted gain from selection (Wright's and Warner's models), and number of effective factors (Wright's, Mather's, and Lande's models). SASQuant makes use of traditional genetic models and allows for their easy application to complex data sets. SASQuant is freely available and is intended for scientists studying quantitative traits in plant populations.
Journal of Heredity 07/2007; 98(4):345-50. · 1.97 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Fruit weight in the cultivated watermelon (Citrullus lanatus (Thunb.) Matsum. & Nakai var. lanatus) ranges from 1 kg to over 100 kg. In recent years, preference of consumers has shifted toward fruit of smaller sizes than the large sizes traditionally used for parties and picnics. This has produced increased interest in the genetics of fruit weight, especially among watermelon breeders. The objectives of this study were to determine the inheritance of fruit weight. Six adapted cultivars having very large or very small fruit weight were crossed in a half diallel. Field trials were conducted at two locations in North Carolina (Clinton and Kinston). Large-fruited parents had higher phenotypic variance than small-fruited parents. Environmental variance was higher than genetic variance (mean, 7.58 and 3.82, respectively) at Kinston, NC. At Clinton, NC, genetic and environmental variances were similar (mean, 9.45 and 8.99, respectively) for 67% of the families. Narrow- and broad-sense heritability estimates were low to intermediate (mean, 0.59 and 0.41, respectively). A high number of effective factors (mean, 5.4) was found to influence fruit weight in watermelon. Watermelon breeders should use quantitative methods such as recurrent selection for population improvement to change fruit weight in the development of new cultivars.
[Show abstract][Hide abstract] ABSTRACT: A bacterial artificial chromosome (BAC) library was constructed for watermelon (Citrullus lanatus (Thunb.) Matsum. & Nakai var. lanatus) with an average insert-size of 106 kb, providing 21 haploid genome equivalents. The library was used to identify BAC clones that are anchored to probes evenly distributed on the genomes of melon or Arabidopsis. Twenty eight probes (representing 66% of the tested probes) from melon and 30 probes (65%) from Arabidopsis identified positive BAC clones. Two methods were implemented to identify SSRs from the positively hybridizing BAC clones. First, analysis of BAC end sequences revealed 37 SSRs. For the second method, pooled DNA of BACs identified by the melon probes was used to develop a shotgun library. The library was then screened with synthetic SSR oligonucleotides by hybridization. Sequence analysis of positively hybridizing shotgun clones revealed 142 different SSRs. Thirty eight SSRs were characterized using three watermelon cultivars, five plant introduction (PI) accessions of C. lanatus var lanatus and four PIs of C. lanatus var citroides. Of these, 36 (95%) were found to be polymorphic with up to six alleles per marker. Polymorphism information content values for polymorphic markers varied between 0.22 and 0.79 with an average of 0.53. The methods described herein will be valuable for the construction of a watermelon linkage map with SSRs evenly distributed on its genome that is anchored to the genomes of melon and Arabidopsis.
Theoretical and Applied Genetics 05/2006; 112(8):1553-62. · 3.51 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai var. lanatus] is a diverse species, with fruits of different sizes, shapes, rind patterns, and flesh colors. This study measured the inheritance of novel rind phenotypes and verified the genetics of white, red, salmon yellow, and canary yellow flesh colors. For each of the 11 crosses, six generations (P(a)S1, P(b)S1, F1, F2, BC1P(a), and BC1P(b)) were produced to form 11 families. Three new genes were identified and designated as follows: Scr for the scarlet red flesh color of Dixielee and Red-N-Sweet, Yb for the yellow belly (ground spot) of Black Diamond Yellow Belly, and ins for the intermittent stripes of Navajo Sweet. The inheritance of the C gene for the canary yellow flesh color was verified as single dominant, and a new inbred type line was developed possessing that gene. Aberrations in the segregation of red, white, and salmon yellow flesh colors were recorded, raising questions on the inheritance of these traits. Finally, the spotted phenotype from Moon and Stars was combined with light green and gray rind patterns for the development of novel cultivars with distinctive rind patterns.
Journal of Heredity 03/2006; 97(2):177-85. · 1.97 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: A new trait, twin fused fruit, was discovered in gynoecious cucumber (Cucumis sativus L.) line B 5263. Plants with the twin fused fruit trait had two fruit fused into a single unit. In addition to having the twin fused fruit trait, line B 5263 had fruit with necks, large tubercles (warts), and dark green skin. The inheritance of twin fused fruit was studied in populations resulting from crosses between gynoecious line B 5263 (twin fused fruit) and monoecious line B 5404 (single fruit). Research was done in 1999 to 2001 in the greenhouses of the Research Institute of Vegetable Crops, Skierniewice, Poland. The F1 progeny developed single fruit in all cases. The observed distribution of plant pheno- types in the F2 fi tted the expected ratio of 3 with single fruit : 1 with twin fused fruit. The observed distribution of plant phenotypes in the BC1A fi tted the expected ratio of 1 with single fruit : 1 with twin fused fruit. Twin fused fruit occurred only in gynoecious plants, and never in monoecious plants of the cross. In the F2 progeny, the ratio of twin fused fruit within gynoecious plants fi tted the expected ratio but the gene was not expressed in monoecious plants. In the F2 generation, the observed distribution of plant phenotypes fi tted the expected ratio of 9 gynoecious single : 4 monoecious single : 3 gynoecious twin fused : 0 monoecious twin fused, indicating that there was epistasis, with twin fused fruit hypostatic to monoecious. The new gene will be named tf (twin fused fruit).