Application of genome-wide insertion/deletion markers on genetic structure analysis and identity signature of Malus acce
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RESEARCH ARTICLE
Open Access
Application of genome-wide insertion/ deletion markers on genetic structure analysis and identity signature of Malus accessions Xuan Wang1, Fei Shen1,2, Yuan Gao3, Kun Wang3, Ruiting Chen1,4, Jun Luo5, Lili Yang5, Xi Zhang1, Changpeng Qiu1, Wei Li1, Ting Wu1, Xuefeng Xu1, Yi Wang1, Peihua Cong3, Zhenhai Han1 and Xinzhong Zhang1*
Abstract Background: Apple (Malus ssp.), one of the most important temperate fruit crops, has a long cultivation history and is economically important. To identify the genetic relationships among the apple germplasm accessions, wholegenome structural variants identified between M. domestica cultivars ‘Jonathan’ and ‘Golden Delicious’ were used. Results: A total of 25,924 insertions and deletions (InDels) were obtained, from which 102 InDel markers were developed. Using the InDel markers, we found that 942 (75.3%) of the 1251 Malus accessions from 35 species exhibited a unique identity signature due to their distinct genotype combinations. The 102 InDel markers could distinguish 16.7– 71.4% of the 331 bud sports derived from ‘Fuji’, ‘Red Delicious’, ‘Gala’, ‘Golden Delicious’, and other cultivars. Five distinct genetic patterns were found in 1002 diploid accessions based on 78 bi-allele InDel markers. Genetic structure analysis indicated that M. domestica showed higher genetic diversity than the other species. Malus underwent a relatively high level of wild-to-crop or crop-to-wild gene flow. M. sieversii was closely related to both M. domestica and cultivated Chinese cultivars. Conclusions: The identity signatures of Malus accessions can be used to determine distinctness, uniformity, and stability. The results of this study may also provide better insight into the genetic relationships among Malus species. Keywords: Malus, InDel, Bud sports, Genetic structure, Germplasm
Background Apple (Malus ssp.), one of the most commonly cultivated fruit crops, supports many local economies in temperate zones. Malus is extremely rich in diversity, with 25 to 78 species in the genus depending on the taxonomic classifications [51, 56]. High levels of interspecific hybridization occur naturally, which generates genetic admixtures, contributing to the diversity within the genus [6, 7, 12]. In addition to the natural diversification * Correspondence: [email protected] 1 College of Horticulture, China Agricultural University, Beijing, China Full list of author information is available at the end of the article
of the genus, anthropogenic activities, including selection and cross breeding, have led to approximately 10,000 cultivars worldwide [8, 21, 65]. Identification of the distinctness of the germplasm would be beneficial to the successful conservation and efficient utilization of genetic resources. The genetic variability and allelic diversity in these accessions are usually examined to reveal their distinctness. Identification of population structure and kinship within germplasm collections is a fundamental prerequisite for identifying robust marker-trait associatio
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