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

Authors: WANG, HUI - Fujian Agricultural & Forestry University; KHERA, PAWAN - University Of Georgia; HUANG, BINGYAN - Henan Agricultural University; YUAN, MEI - Shandong Academy Of Agricultural Sciences; KATAM, RAMESH - Florida A & M University; ZHUANG, WEIJIAN - Fujian Academy; Harris-Shultz, Karen; MOORE, KIM - Agresearch Consultants; CULBREATH, ALBERT - University Of Georgia; ZHANG, XINYOU - Henan Agricultural University; VARSHNEY, RAJEE - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; XIE, LIANHUI - Fujian Academy; Guo, Baozhu

Submitted to: Journal of Integrative Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/10/2015
Publication Date: 4/30/2016
Citation: Wang, H., Khera, P., Huang, B., Yuan, M., Katam, R., Zhuang, W., Harris-Shultz, K.R., Moore, K.M., Culbreath, A.K., Zhang, X., Varshney, R.K., Xie, L., Guo, B. 2016. Analysis of genetic diversity and population structure of peanut cultivars and breeding lines from China, India and the US using SSR markers. Journal of Integrative Plant Biology. 58:452-465. doi: 10.1111/jipb.12380.

Interpretive Summary: During the years, efforts have been made to improve peanut yield, quality, and disease resistance resulting in great improvement of many traits in peanut. However, it is sometimes difficult to choose parents for hybridization solely based on their morphological features. Hence the knowledge of genetic diversity among released and pre-released peanut cultures is very important for germplasm utilization in peanut breeding. The objectives of this study were to select a set of highly polymorphic SSR markers which could be used in the assessment of genetic diversity among peanut germplasm and breeding lines in each breeding program, and to assess the levels of genetic diversity and population structure of peanut lines used in each breeding programs. The 111 SSR markers were useful in determining the genetic relationships and diversity of 79 peanut breeding lines. The mean values of gene diversity and polymorphic information content (PIC) were 0.480 and 0.429, respectively. Country-wise analysis revealed that alleles per locus in three countries were similar. The mean gene diversity in the US, China and India was 0.363, 0.489 and 0.47 with an average PIC of 0.323, 0.43 and 0.412, respectively. Genetic analysis using the STRUCTURE divided these peanut lines into two populations (P1, P2), which was consistent to the dendrogram based on genetic distance (G1, G2) and the clustering of principal component analysis. The groupings were related to peanut market types and the geographic origin with a few admixtures. The results could be used by breeding programs to assess the genetic diversity of breeding materials to broaden the genetic base and for molecular genetics studies.

Technical Abstract: Cultivated peanut is grown worldwide as rich-source of oil and protein. A broad genetic base is needed for cultivar improvement. The objectives of this study were to develop highly informative simple sequence repeat (SSR) markers and to assess the genetic diversity and population structure of peanut cultivars and breeding lines from different breeding programs in China, India and the US. A total of 111 SSR markers were selected for this study, resulting in a total of 472 alleles. The mean values of gene diversity and polymorphic information content (PIC) were 0.480 and 0.429, respectively. Country-wise analysis revealed that alleles per locus in three countries were similar. The mean gene diversity in the US, China and India was 0.363, 0.489 and 0.47 with an average PIC of 0.323, 0.43 and 0.412, respectively. Genetic analysis using the STRUCTURE divided these peanut lines into two populations (P1, P2), which was consistent to the dendrogram based on genetic distance (G1, G2) and the clustering of principal component analysis. The groupings were related to peanut market types and the geographic origin with a few admixtures. The results could be used by breeding programs to assess the genetic diversity of breeding materials to broaden the genetic base and for molecular genetics studies.