DArTseq Genotypic and Phenotypic Diversity of Barley Landraces Originating from Different Countries

Abstract

Landraces are considered a key element of agrobiodiversity because of their high variability and adaptation to local environmental conditions, but at the same time, they represent a breeding potential hidden in gene banks that has not yet been fully appreciated and utilized. Here, we present a genome-wide DArTseq analysis of the diversity of 116 spring barley landraces preserved in the collection of the Polish gene bank. Genetic analysis revealed considerable variation in this collection and several distinct groups related to the landraces’ country of origin and the grain type were identified. The genetic distinctness of hulless accessions may provide a basis for pro-quality breeding aimed at functional food production. However, the variable level of accession heterogeneity can be a significant obstacle. A solution to this problem is the establishment of special collections composed of pure lines that are accessible to breeders. Regions lacking genetic diversity have also been identified on 1H and 4H chromosomes. A small region of reduced heterogeneity was also present in the hulless forms in the vicinity of the nud gene that determines the hulless grain type. However, the SNPs present in this area may also be important in selection for traits related to grain weight and size because their QTLs were found there. This may support breeding of hulless forms of spring barley which may have applications in the production of high-quality foods with health-promoting values.

Genetic Diversity and Population Structure Analysis of Barley Landraces from Shanghai Region Using Genotyping-by-Sequencing

“…The genetic diversity analysis for the barley landrace collection in this study identified a total of 210,268 SNPs, which would be impossible by previous methods. The SNPs were distributed almost throughout the whole genome despite they were more density toward the telomeric chromosome regions, and this was also found in other reports [7,37]. Therefore, the results based on these SNP markers will be more accurate and useful.…”

“…The two kinds of molecular markers of SSR and SNP are the most commonly used in barley genetic diversity analysis [4][5][6][7][8]15,[26][27][28][29][30][31][32][33][34]. SSR markers were once very popular because of their good stability and easy operation.…”

“…SNP-based loci detection is best based on nucleotide sequencing, but sequencing costs were once so high that it was impossible to analyze genetic diversity by nucleotide sequence analysis of every individual in a barley population. Therefore, PCR amplification-based detection of SNP loci combined with gene chip or DNA array technology was used [5,7,26,27,30,32,33,35,36]. The polymorphic markers that could be identified and used by this method were still limited.…”

“…Barley is a self-pollinated crop, and some are even cleistogamous, so conventional barley varieties are highly inbred and largely homozygous, while barley landraces may be less so [1,7]. The landraces in this study have undergone multiple generations of self-pollination, including single-seed propagation, so could be expected to be very close to homozygosity.…”

“…Barley is also used as a model plant for the Triticeae tribe because of its diploid characteristics [2,3]. However, modern barley cultivars, like other crops, are suffering problems caused by narrowed genetic backgrounds, and these problems are aggravated by climate change and frequent extreme weather events [4][5][6][7]. Thus, it is necessary to collect and utilize more barley germplasms to meet the requirements of barley breeding in the future.…”