Genetic diversity, germplasm identification and population structure of Diospyros kaki Thunb. from different geographic regions in China using SSR markers

Guan, Changfei; Zhang, Pingxian; Hu, Chaoqiong; Chachar, Sadaruddin; Riaz, Adeel; Wang, Renzi; Yang, Yong

doi:10.1016/j.scienta.2019.02.062

Cited by 27 publications

(24 citation statements)

References 39 publications

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“…Our results showed a mean observed heterozygosity ( Ho ) of 0.6, which is highly consistent with the study of Soriano et al [ 15 ] that detected an observed heterozygosity for selected SSRs in the range of 0.27–0.83 [ 15 ]. The level of polymorphic alleles in the D. kaki collection was also high, with P = 100% based on eight SSRs used, and comparable to other studies on Diospyros [ 6 , 14 , 16 ]. However, many markers were not efficient and SSRs are limited for Diospyros genotyping [ 19 , 41 ].…”

Section: Discussionsupporting

confidence: 85%

“…In contrast, we observed the clear separation of D. kaki germplasm into two different clusters using SSR and ISSR markers. Another study on D. kaki germplasm using SSR, IRAP and SCoT markers separated 228 accessions into five genetic clusters mostly based on geographical origin [ 6 , 19 ]. In comparison, our results revealed lower cluster numbers in our D. kaki collection.…”

Section: Discussionmentioning

confidence: 99%

“…The wild species D. virginiana (American persimmon) is native to the USA and usually used as timber wood. This species is important as a genetic resource and is usually crossed with D. kaki in breeding programs aimed at cold tolerance and early harvesting [ 6 , 7 ].…”

Section: Introductionmentioning

confidence: 99%

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Genetic Diversity in Diospyros Germplasm in the Western Caucasus Based on SSR and ISSR Polymorphism

Самарина

Malyarovskaya

Reim

et al. 2021

Biology

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Persimmon germplasm in the Western Caucasus represent one of the most northerly collections. In our study, 51 commercial cultivars of D. kaki, 3 accessions of D. virginiana and 57 D. lotus accessions from six geographically distant populations were investigated using 19 microsatellite and 10 inter simple sequence repeat (ISSR) markers. After STRUCTURE analysis, the single accessions of Diospyros were allocated to three genetic clusters. Genetic admixtures in the important genotypes of D. kaki were revealed, whereas D. lotus accessions showed no admixture with other genetic clusters. The correspondence of genetic data and phenotypical traits was estimated in the D. kaki collection. The most frost tolerant genotypes of the collection, such as “Mountain Rogers”, “Nikitskaya Bordovaya”, “Rossiyanka”, “MVG Omarova”, “Meader”, “Costata”, “BBG”, and “Jiro”, showed a high percentage of genetic admixtures and were grouped close to D. virginiana. Some of these genotypes are known to be interspecific hybrids with D. virginiana. A low level of genetic diversity between the distant D. lotus populations was revealed and it can be speculated that D. lotus was introduced to the Western Caucasus from a single germplasm source. These results are an important basis for the implementation of conservation measures, developing breeding strategies, and improving breeding efficiency.

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Section: Discussionsupporting

confidence: 85%

Section: Discussionmentioning

confidence: 99%

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Genetic Diversity in Diospyros Germplasm in the Western Caucasus Based on SSR and ISSR Polymorphism

Самарина

Malyarovskaya

Reim

et al. 2021

Biology

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“…High polymorphism was revealed with considerable differentiation between Chinese and Japanese accessions. In another study, 228 persimmon accessions from five different regions in China were investigated with 12 SSR loci [ 102 ]. The five groups produced by a cluster analysis contained accessions from different regions, suggesting considerable gene flow.…”

Section: Genetic Diversitymentioning

confidence: 99%

Recent Large-Scale Genotyping and Phenotyping of Plant Genetic Resources of Vegetatively Propagated Crops

Nybom

Lācis

2021

Plants

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Several recent national and international projects have focused on large-scale genotyping of plant genetic resources in vegetatively propagated crops like fruit and berries, potatoes and woody ornamentals. The primary goal is usually to identify true-to-type plant material, detect possible synonyms, and investigate genetic diversity and relatedness among accessions. A secondary goal may be to create sustainable databases that can be utilized in research and breeding for several years ahead. Commonly applied DNA markers (like microsatellite DNA and SNPs) and next-generation sequencing each have their pros and cons for these purposes. Methods for large-scale phenotyping have lagged behind, which is unfortunate since many commercially important traits (yield, growth habit, storability, and disease resistance) are difficult to score. Nevertheless, the analysis of gene action and development of robust DNA markers depends on environmentally controlled screening of very large sets of plant material. Although more time-consuming, co-operative projects with broad-scale data collection are likely to produce more reliable results. In this review, we will describe some of the approaches taken in genotyping and/or phenotyping projects concerning a wide variety of vegetatively propagated crops.

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“…However, these methods are easily affected by environmental conditions and developmental stages (Luo et al, 2001). Fortunately, DNA molecular marker techniques are able to overcome these limitations and act as powerful tools for evaluating genetic diversity and relationships (Guan et al, 2019;Queiroz et al, 2015;Riaz et al, 2018). Therefore, a variety of molecular markers, such as random amplified polymorphic DNA (Luo et al, 2001)], intersimple sequence repeat Zhang et al, 2011)], sequence-related amplified polymorphism (SRAP) (Liu et al, 2013), and SSR Liu et al, 2012)], have been used recently to examine the genetic diversity and relationships among wild Chinese grape species.…”

mentioning

confidence: 99%

Genetic Diversity and Population Structure Analysis of Chinese Wild Grape Using Simple Sequence Repeat Markers

Li¹,

Fan²,

Zhang³

et al. 2021

J. Amer. Soc. Hort. Sci.

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Chinese wild Vitis is a useful gene source for resistance to biotic and abiotic stresses, although there is little research on its genetic diversity and structure. In this study, nine simple sequence repeat (SSR) markers were used to assess the genetic diversity and genetic structure among 100 Vitis materials. These materials included 77 indigenous accessions representing 23 of 38 wild Vitis species/cultivars in China, 18 V. vinifera cultivars, and the five North American species V. aestivalis, V. girdiana, V. monticola, V. acerifolia, and V. riparia. The SSR loci used in this study for establishing an international database (Vitis International Variety Catalogue) revealed a total of 186 alleles in 100 Vitis accessions. The mean values for the gene diversity (GD) and polymorphism information content (PIC) per locus were 0.91 and 0.90, respectively, which indicates that the discriminatory power of the markers is high. Based on the genetic distance data, the 100 Vitis accessions were divided into five primary clusters by cluster analysis, and five populations by structure analysis; these results indicate these Chinese wild grapes were more genetically close to European grapes than to North American species. In addition, the clustering patterns of most accessions correlated with the geographic distribution. An analysis of molecular variance (AMOVA) revealed that 3.28%, 3.27%, and 93.46% of the variance occurred between populations, between individuals within populations, and between individuals within the entire population, respectively. In addition, we identified three previously undescribed accessions (Wuzhi-1, MZL-5, and MZL-6) by cluster analysis. Our results reveal a high level of genetic diversity and variability in Vitis from China, which will be helpful in the use of genetic resources in future breeding programs. In addition, our study demonstrates that SSR markers are highly suitable for further genetic diversity analyses of Chinese wild grapes.

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Genetic diversity, germplasm identification and population structure of Diospyros kaki Thunb. from different geographic regions in China using SSR markers

Cited by 27 publications

References 39 publications

Genetic Diversity in Diospyros Germplasm in the Western Caucasus Based on SSR and ISSR Polymorphism

Genetic Diversity in Diospyros Germplasm in the Western Caucasus Based on SSR and ISSR Polymorphism

Recent Large-Scale Genotyping and Phenotyping of Plant Genetic Resources of Vegetatively Propagated Crops

Genetic Diversity and Population Structure Analysis of Chinese Wild Grape Using Simple Sequence Repeat Markers

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