Analysis of spatial distribution of genetic diversity and validation of Indian foxtail millet core collection

Abstract

Foxtail millet [ (L.) P. Beauv.] is an important small millet, grown as a short duration, drought tolerant crop across the world. This crop can be grown on wide ranges of soil conditions and has an immense potential for food and fodder in rainfed and arid regions of the India. In the present study, 31 primer pairs (27 SSR and 4 EST-SSR) were used to analyse the genetic diversity in 223 core collection accessions. Analysis resulted in detection of a total of 136 alleles with an average of 4.38 alleles per locus. Among these 136 alleles, 22 were rare, 70 were common and 44 were frequent. The PIC value ranged from 0.01 to 0.86 with an average of 0.31. The average number of observed alleles ranged from 2.0 (northern hills of India accessions) to 4.06 (exotic) with an average of 2.72. The mean Shannon's Information Index ranged from 0.44 (northern hills of India) to 0.69 (exotic) with an average of 0.52. Pair-wise Fst values indicated little to moderate genetic differentiation among the group of accessions. UPGMA clustering grouped the accessions into two major groups while analysis for population substructure indicated presence of four subpopulations. However there was no statistically well supported grouping of the accessions based on eco-geographic specificities. The core collection designated here represented substantial genetic diversity at molecular level, hence may be a good source of diversity for use in foxtail improvement programs in the region.

Population structure, marker-trait association and identification of candidate genes for terminal heat stress relevant traits in bread wheat (Triticum aestivum L. em Thell)

“…The PIC values and an average number of alleles per locus have shown a strong positive association with each other, which is following the earlier studies. Trends of increasing genetic diversity based on higher PIC values were also reported by earlier researchers (Ramya et al, 2015;Chander et al, 2017). The selected genotypes were grouped into two major clusters collected from different regions having tolerant, intermediate and sensitive response towards HS.…”

“…Trends of increasing genetic diversity based on higher PIC values were also reported by earlier researchers (Ramya et al ., 2015; Chander et al ., 2017). The selected genotypes were grouped into two major clusters collected from different regions having tolerant, intermediate and sensitive response towards HS.…”

Domestication and Improvement in the Model C4 Grass, Setaria

“…Height is a trait that may be targeted by human selection during crop domestication and improvement, and there is significant variation in height in landrace varieties of foxtail millet, and within green foxtail accessions ( Li and Yang, 2008 ; Chander et al, 2017a , b ; Ghimire et al, 2018 ). Differences in height amongst landrace varieties may reflect both an ancestral increase in height took place as selection for losing unproductive tillers, followed by differentiation as farmers in different localities targeted height for a variety of reasons, including grain production and foraging.…”

Assessing Genetic Diversity among Foxtail millet (Setaria italica (L.) P. Beauv.) Accessions Using RAPD and ISSR Markers

“…Morphological characterization does not reliably portray the genetic relationships among the genotypes because of environmental interactions, unknown genetic control of the traits and inadequate sampling of the genome in terms of phenotype. Thus, for genetic diversity assessment, molecular markers offer considerable advantages over the morphological markers (Reddy et al, 2006;Chander et al, 2017;Ramesh et al, 2017). The diversity studies at molecular level in foxtail millet are very meagre and were mainly based on RFLP analysis (Fukunaga et al, 2002), using these markers they have concluded that the foxtail millet landrace belonging to China were more variable.…”

“…During our investigation also the co-dominant markers were not available; the analysis was done using ISSR and RAPDs. In last 4-5 years number of studies have been performed using SSR and EST-SSRs for genetic diversity analysis in foxtail millet ( Goron and Raizada, 2015, Ali et al, 2016, Wang et al, 2016, Andesen and Nepal, 2017, Chander et al, 2017.…”