Use of VeraCode 384-plex assays for watermelon diversity analysis and integrated genetic map of watermelon with single nucleotide polymorphisms and simple sequence repeats

Nimmakayala, Padma; Abburi, Venkata Lakshmi; Bhandary, Abhishek; Abburi, Lavanya; Vajja, Venkata Gopinath; Reddy, Rishi; Malkaram, Sridhar A.; Pegadaraju, Venkatramana; Wijeratne, Asela J.; Tomason, Yan R.; Levi, Amnon; Wehner, Todd C.; Reddy, Umesh K.

doi:10.1007/s11032-014-0056-9

Cited by 24 publications

(24 citation statements)

References 48 publications

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“…The genetic parameters such as gene diversity, PIC, and heterozygosity were lowest in East Asian ecotypes (Pop IB), were higher in American and East Asian ecotypes mixed (Pop IA), and highest in American ecotypes (Pop IIA). However, this observation was inconsistent from results obtained by Nimmakayala et al (2014) who placed these two ecotypes into a single group. The discrepancy may be due to the difference in sampling sizes used by the two studies.…”

Section: Resultscontrasting

confidence: 69%

“…From a plant breeding perspective, molecular analysis can help to define the lineage relationships among genetic materials and to eliminate the phenomenon of homonyms as well as aiding identification of breeding lines carrying genes of interest (Hu et al, 2014). In watermelon, molecular markers have been used for fingerprinting, identifying and characterizing watermelon genotypes, and examining population structure (Levi et al, 2013;Mujaju et al, 2010;Nantoum e et al, 2013;Nimmakayala et al, 2014;Zhang et al, 2012). Nevertheless, a broader understanding of the diversity and differentiation among and within Citrullus accessions is still lacking; also, there seems to be no information available on the overall genetic diversity and population structure of a wide spectrum of watermelon accessions.…”

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confidence: 99%

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Genetic Diversity, Population Structure, and Formation of a Core Collection of 1197 Citrullus Accessions

Zhang¹,

Fan²,

Guo³

et al. 2016

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Watermelon belongs to the genus Citrullus. There have been continuing interests in breeding of watermelon for economic benefits, but information on the scope and utilization of genetic variations in Citrullus is still limited. The present study was conducted in 2012–13, to evaluate the genetic diversity and population structure of the 1197 line watermelon collection maintained by the Beijing Vegetable Research Center (BVRC), which belongs to seven Citrullus species including Citrullus naudinianus, Citrullus colocynthis, Citrullus rehmii, Citrullus ecirrhosus, Citrullus amarus, Citrullus mucosospermus, and Cirullus lanatus subsp. vulgaris. Twenty-three highly informative microsatellite markers evenly distributed in the watermelon genome were used to assess genetic diversity in this collection. The markers detected on an average of 6.05 alleles per locus with the average value of polymorphism information content (PIC) at 0.49. A high level of gene diversity [Nei’s gene diversity index (Nei) = 0.56] and a low observed heterozygosity (Ho = 0.10) were revealed within the collection. Structure analysis grouped the 1197 accessions into two main populations (Pop I and Pop II) and an admixture group. Pop I contained 450 accessions from C. lanatus subsp. vulgaris (446) and C. mucosospermus (4). Pop II comprised 465 accessions, 379 of which belonged to C. lanatus subsp. vulgaris and 86 to C. naudinianus (3), C. ecirrhosus (2), C. rehmii (2), C. colocynthis (11), C. amarus (58), and C. mucosospermus (10). The remaining 282 accessions were classified as an admixture group. The two main populations were further subdivided into four subgroups. The groupings were consistent with the estimation of F statistics (Fst) and Nei’s genetic distances in collections. We confirmed the distinct genetic backgrounds between American and East Asian ecotypes. Subsequently, we defined a core set consisting of 130 accessions including 47 from Pop I, 68 from Pop II, and 15 from the Admixture group. This core set was able to capture all 133 alleles detected by 23 simple sequence repeats (SSRs) in 1197 accessions. These results will facilitate efficient use of genetic variations in Citrullus in watermelon breeding and help optimization of accessions in genomewide association studies.

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confidence: 69%

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confidence: 99%

Genetic Diversity, Population Structure, and Formation of a Core Collection of 1197 Citrullus Accessions

Zhang¹,

Fan²,

Guo³

et al. 2016

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“…[3][4][5] Dessert modern watermelon has a narrow genetic base. [6][7][8] Landraces can provide importants traits for tolerance to drought and heat, such as higher biomass, which would greatly improve the crop's adaptation to climate change worldwide. 9 Identification of watermelon germplasm with drought tolerance properties is needed for the development of drought tolerant watermelon varieties.…”

Section: Introductionmentioning

confidence: 99%

Genotypic variability in fruits characters of moroccan watermelon cultivars (Citrullus Lanatus) cultivars under well and limited watered conditions

Said¹,

Fatiha²

2018

HIJ

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“…Levi et al (2001b) found that 46 American cultivars varied by 0.4% to 8%. East Asian and American cultivar types were found to be genetically similar by some analyses (Nimmakayala et al, 2014a;Reddy et al, 2015) but as distinct ecotypes in others (Guo et al, 2013;Zhang et al, 2012). The resequencing of 20 watermelon accessions shows that watermelon is less genetically diverse than maize, soybean, and rice (Guo et al, 2013).…”

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confidence: 94%

“…As such, estimates of genotypic variation among cultivars have been low. The genetic diversity among 130 edible-type accessions sampled throughout the world was estimated at 5% (Nimmakayala et al, 2014a). Levi et al (2001b) found that 46 American cultivars varied by 0.4% to 8%.…”

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confidence: 99%

Inter- and Intracultivar Variation of Heirloom and Open-pollinated Watermelon Cultivars

Stone¹,

Boyhan²,

McGregor³

2019

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Additional index words. genotypic, phenotypic, simple sequence repeat Abstract. Watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai] cultivars exhibit diverse phenotypic traits, yet are derived from a narrow genetic base. Heirloom cultivars, and to a lesser extent modern open-pollinated (OP) cultivars, are perceived to contain vital genetic variation that is critical for biodiversity conservation and crop improvement. The objective of this study was to characterize the diversity of six heirloom and open-pollinated watermelon cultivars that are popular among U.S. organic, directmarket, and home gardeners. An additional evaluation was conducted to determine whether significant phenotypic and genotypic variation existed among seed lots sourced from different commercial seed vendors. Important horticultural traits such as days to germination, days to first flower, yield, and fruit quality were measured over two field seasons. Genetic diversity was estimated using 32 simple sequence repeat (SSR) markers. Significant differences in horticultural traits among seed lots in both years were observed only in days to germination and first male flower, which may be a consequence of vendor differences in seed storage and quality control. Heirloom 'Moon and Stars' and modern OP 'Sugar Baby' were the most genetically distinct from the other cultivars and heirloom 'Georgia Rattlesnake' was determined to be highly related to the modern OP 'Charleston Gray'. The two heirloom cultivars were observed to have lower average gene diversity than the modern cultivars. Heirloom 'Moon and Stars' contained significant genetic variation among seed lots, yet heirloom 'Georgia Rattlesnake' contained none. These findings suggest that genetic variation can be more accurately attributed to pedigree and foundation seed maintenance practices than to the ''heirloom'' designation per se. The variation reported in this study can be used to inform conservation and breeding efforts.

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Use of VeraCode 384-plex assays for watermelon diversity analysis and integrated genetic map of watermelon with single nucleotide polymorphisms and simple sequence repeats

Cited by 24 publications

References 48 publications

Genetic Diversity, Population Structure, and Formation of a Core Collection of 1197 Citrullus Accessions

Genetic Diversity, Population Structure, and Formation of a Core Collection of 1197 Citrullus Accessions

Genotypic variability in fruits characters of moroccan watermelon cultivars (Citrullus Lanatus) cultivars under well and limited watered conditions

Inter- and Intracultivar Variation of Heirloom and Open-pollinated Watermelon Cultivars

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