Genetic Diversity and Population Structure of the Major Peanut (Arachis hypogaea L.) Cultivars Grown in China by SSR Markers

Abstract

One hundred and forty-six highly polymorphic simple sequence repeat (SSR) markers were used to assess the genetic diversity and population structure of 196 peanut (Arachis Hypogaea L.) cultivars which had been extensively planted in different regions in China. These SSR markers amplified 440 polymorphic bands with an average of 2.99, and the average gene diversity index was 0.11. Eighty-six rare alleles with a frequency of less than 1% were identified in these cultivars. The largest Fst or genetic distance was found between the cultivars that adapted to the south regions and those to the north regions in China. A neighbor-joining tree of cultivars adapted to different ecological regions was constructed based on pairwise Nei’s genetic distances, which showed a significant difference between cultivars from the south and the north regions. A model-based population structure analysis divided these peanut cultivars into five subpopulations (P1a, P1b, P2, P3a and P3b). P1a and P1b included most the cultivars from the southern provinces including Guangdong, Guangxi and Fujian. P2 population consisted of the cultivars from Hubei province and parts from Shandong and Henan. P3a and P3b had cultivars from the northern provinces including Shandong, Anhui, Henan, Hebei, Jiangsu and the Yangtze River region including Sichuan province. The cluster analysis, PCoA and PCA based on the marker genotypes, revealed five distinct clusters for the entire population that were related to their germplasm regions. The results indicated that there were obvious genetic variations between cultivars from the south and the north, and there were distinct genetic differentiation among individual cultivars from the south and the north. Taken together, these results provided a molecular basis for understanding genetic diversity of Chinese peanut cultivars.

Analysis of genetic diversity and population structure of peanut cultivars and breeding lines from China, India and the US using simple sequence repeat markers

“…The 111 SSRs detected a total of 472 alleles, the number of alleles per marker detected ranged from 2 to 9 with an average of 4.25 per locus and this result is in agreement with those of the previous genetic diversity studies. Ren et al () reported the results of 2 to 9 alleles with an average of 3.0 alleles per locus, Roomi et al () resulted in 2 to 4 alleles with an average of 2.6 alleles per locus, and Pandey et al () observed 2 to 14 alleles per locus with an average of 3.2. Most of the studies reported 2–8 alleles per locus, compared to higher alleles of 2–13 alleles of Song et al (), 2–20 alleles of Varshney et al () and 3–15 alleles of Naito et al ().…”

“…In this study, most of the peanut lines were released cultivars, and some were breeding lines, so the allele number per locus would be similar to that of released cultivars (Jiang et al ). There is a report suggesting that there is less genetic diversity in released cultivars than landraces (Ren et al ). This study is in agreement with Ren et al () that the 111 SSR markers are effective and useful for analyzing the genetic diversity of peanut breeding lines, germplasm, and released cultivars.…”

“…Hence the knowledge of genetic diversity among released and pre‐released peanut cultures is very important for germplasm utilization in peanut breeding. To broaden the genetic variation of cultivated peanut in future breeding programs, it is necessary to perform a more comprehensive study of genetic diversity and population structure of the peanut varieties (Ren et al ). Therefore, research on the genetic diversity among cultivars is necessary for a more efficient and successful hybridization program because crosses involving more diverse parents are likely to produce higher heterotic effects and also more variability in the segregating generations (Suneetha et al ).…”

Utility of AhTE Markers for Genetic and Genomic Studies in Groundnut (Arachis hypogaea L.)

“…AhTE markers could be successfully used to group the genotypes based on the principal co-ordinates. Therefore, AhTE markers might provide an efficient marker system, like SSR markers (Li et al, 2011;Ren et al, 2014), for genetic and genomic studies in groundnut. Recently, AhTE markers have been successfully employed for trait mapping in groundnut (Shirasawa et al, 2012b;Kolekar et al, 2016).…”

First microsatellite markers forScaligeria lazicaBoiss. (Apiaceae) by next-generation sequencing: population structure and genetic diversity analysis

“…To identify the true optimal number of subsets (K) in STRUCTURE, LnP(D) and DK were chosen, as described in Ren et al [45]. The K value that provides the maximum likelihood, called LnP(D) in STRUCTURE, is generally considered as the optimal number of subdivisions [37].…”