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

Abstract

Barley (Hordeum vulgare L.) is an important economic crop for food, feed and industrial raw materials. In the present research, 112 barley landraces from the Shanghai region were genotyped using genotyping-by-sequencing (GBS), and the genetic diversity and population structure were analyzed. The results showed that 210,268 Single Nucleotide Polymorphisms (SNPs) were present in total, and the average poly-morphism information content (PIC) was 0.1642. Genetic diversity and population structure analyses suggested that these barley landraces were differentiated and could be divided into three sub-groups, with morphological traits of row-type and adherence of the hulls the main distinguishing factors between groups. Genotypes with similar or duplicated names were also investigated according to their genetic backgrounds and seed appearances. This study provided valuable information on barley landraces from the Shanghai region, and showed that all these barley landraces should be protected and used for future breeding programs.

Genetic Diversity and Genome-Wide Association Analysis of the Hulled/Naked Trait in a Barley Collection from Shanghai Agricultural Gene Bank

“…In addition, compared with our previous work [9], it was found that the classification based on the phylogenetic tree was similar, whereas in the population structure analysis, two sub-populations dominated by two-rowed barley varieties appeared, indicating that it might be affected by other factors in addition to morphological characters, such as geographical location and growth habits [12].…”

“…The hulled/naked trait was directly observed from the seeds and the row type was observed in the field at the maturity stage. The information of the first 112 barley genotypes was reported previously [9], and that of the last 71 barley genotypes is listed in Table 2.…”

“…Total genomic DNA isolation and sequencing-library construction for SNP arrays were performed mainly according to Li et al [9]. GBS was conducted on the Illumina Nova platform (Illumina Inc., San Diego, CA, USA) by Oebiotech Company (Shanghai, China), and 150 bp pair-end raw reads were generated.…”

“…The local alignment of the clean reads of the newly studied 71 barley genotypes (NCBI accession number PRJNA941018) and the previously studied 112 barley genotypes (NCBI accession number PRJNA814403) to the reference genome of barley cv. Morex (V2) was conducted using BWA software (v0.7.17) [9], and the reference genome had been previously downloaded from Ensembl Plants. SNP calling was performed using the HaplotypeCaller module of Genome Analysis Tool Kit (GATK) software (v4.1.3) and only SNP markers with QualByDepth (QD) ≥ 2 were preserved [15].…”

“…A large number of barley germplasm samples have been collected and preserved, and they play an important role in barley breeding in the region. Previously, we used simple sequence repeat (SSR) markers and genotyping-by-sequencing (GBS)-based SNP markers to analyze the genetic background of 112 barley landraces, and these genotypes can be divided into three clusters according to the phylogenetic tree, which seem to be consistent with the classification according to the traits of row type and hulled/naked character [8,9]. In addition, the problem of duplicate names was also solved, based on their different genetic backgrounds, which will be more conducive to the protection and utilization of these germplasm resources.…”