Population structure and linkage disequilibrium in six-rowed barley landraces from the Qinghai-Tibetan Plateau

Abstract

The genetic diversity, population structure, and extent of linkage disequilibrium (LD) were investigated at a genome-wide level in 255 six-rowed barley (Hordeum vulgare L. ssp. Vulgare) landraces from the Qinghai-Tibetan Plateau using 1264 polymorphic diversity array technology (DArT) markers. The mean polymorphism information content (PIC) of the DArT markers ranged between 0.008 and 0.500 with an average of 0.213. Bayesian, principal coordinate analysis, and phylogenetic analysis supported that six-rowed barley landraces from this region are divided into five distinct subpopulations centered on the regions of origin of the germplasm. The genetic distances calculated for all the individual pairs were geographically dependent, as revealed by Mantel tests (r = 0.35, P < 0.001) and spatial autocorrelation analysis. The LD values, expressed as r2, declined with increasing genetic distance, and the same tendency occurred on each chromosome. In general, LD values were low (9.1% of adjacent markers; P < 0.001), and mean LD values across the whole genome decayed to below the critical r2 of 0.22 after 3.32 cM. Approximately 19.0% of marker pairs (mean r2 = 0.586) located on the same chromosome and 4.9% of pairs (mean r2 = 0.318) located on different chromosomes were in LD (r2 ≥ 0.22). Our results discerned relevant patterns of genetic diversity, population structure, and LD among members of a Qinghai-Tibet Plateau barley landraces panel proposed to be 'typical' of a target region or environment and have important implications for further studies on association mapping and practical breeding in high-altitude naked barley. © Crop Science Society of America.