Features of SNP and SSR diversity in a set of ICARDA barley germplasm collection |
| |
Authors: | R K Varshney M Baum P Guo S Grando S Ceccarelli A Graner |
| |
Institution: | (1) Leibniz Institute of Plant Genetics & Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany;(2) International Centre for Agricultural Research in Dry Areas (ICARDA), P.O. Box 5466, Aleppo, Syria;(3) College of Life Science, Guangzhou University, 510006 Guangzhou, China;(4) International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Greater Hyderabad, AP, 502324, India |
| |
Abstract: | Detection and utilization of genetic variation available in the germplasm collection for crop improvement have been the prime
activities of breeders. Here a set of ICARDA barley germplasm collection comprising of 185 cultivated (Hordeum vulgare L.) and 38 wild (H. spontaneum L.) genotypes originated from 30 countries of four continents was genotyped with 68 single nucleotide polymorphism (SNP)
and 45 microsatellite or simple sequence repeat (SSR) markers derived from genes (expressed sequence tags, ESTs). As two SNP
markers provided 2 and 3 datapoints, a total of 71 SNPs were surveyed that yielded a total of 143 alleles. The number of SSR
alleles per locus ranged from 3 to 22 with an average of 7.9 per marker. Average PIC (polymorphism information content) value
for SSR and SNP markers were recorded as 0.63 and 0.38, respectively. Heterogeneity was recorded at both SNP and SSR loci
in an average of 5.72 and 12.42% accessions, respectively. Genetic similarity matrices for SSR and SNP allelic data were highly
correlated (r = 0.75, P < 0.005) and therefore allelic data for both markers were combined and analyzed for understanding the genetic relationships
among the germplasm surveyed. Majority of clusters/subclusters were found to contain genotypes from the same geographic origins.
While comparing the genetic diversity, the accessions coming from Middle East Asia and North East Asia showed more diversity
as compared to that of other geographic regions. Majority of countries representing Africa, Middle East Asia, North East Asia
and Arabian Peninsula included the genotypes that contained rare alleles. As expected, spontaneum accessions, as compared to vulgare accessions, showed a higher number of total alleles, higher number of alleles per locus, higher effective number of alleles
and higher allelic richness and a higher number of rare alleles were observed. In summary, the examined ICARDA germplasm set
showed ample natural genetic variation that can be harnessed for future breeding of barley as climate change and sustainability
have become important throughout all growing areas of the world, drought/heat tolerance being the most important ones. |
| |
Keywords: | |
本文献已被 SpringerLink 等数据库收录! |
|