Association mapping for agronomic traits in six-rowed spring barley from the USA harvested in Kazakhstan

Abstract

In barley, six-rowed barley is advantageous over two-rowed barley for feed due to the larger number of seeds per spike and the higher seed protein content. The growth of six-rowed barley is potentially important for breeding in agriculturally oriented countries, such as Kazakhstan. Nevertheless, until recently, very little attention was given to six-rowed barley in breeding projects in Kazakhstan, one of the largest countries in the world. In this study, phenotyping and single nucleotide polymorphism (SNP) genotyping data were generated from 275 accessions originating from six different breeding organizations in the USA as well as 9 accessions from Kazakhstan in field trials at six breeding institutions. The USA six-rowed barley was tested in comparison to local accessions over three years (2009–2011) based on analyses of key agronomic traits. It was determined that the average yield in the USA accessions in comparison to local lines showed heavier yield in all six tested sites. Principal Coordinate Analysis based on 1618 polymorphic SNP markers separated Kazakh lines from six USA barley origin groups based on PC1 (77.9%), and Montana lines from the remaining five USA groups based on PC2 (15.1%). A genome-wide association study based on eighteen field trials allowed the identification of 47 stable marker-trait associations (MTA) for ten agronomic traits, including key yield related characters such as yield per square meter, thousand grain weight, number of kernels per spike, and productive tillers. The comparison of chromosomal positions of identified MTA with positions of known genes and quantitative trait loci suggests that 25 out of those 47 MTAs are presumably novel. The analysis of 42 SNPs associated with 47 MTAs in the Ensemble genome annotation system ( http://ensemblgenomes.org ) suggested that 40 SNPs were in genic positions of the genome, as their sequences successfully aligned with corresponding Gen ID.

Quantitative trait loci for agronomic traits in tetraploid wheat for enhancing grain yield in Kazakhstan environments

“…Although GWAS has proven to be very effective for capturing relevant marker-trait associations (MTAs) for yield components, results reported from studies in different regions of the world are revealing the tendency for a strong influence of the environmental conditions with significant genotype x environment interaction (GEI) revealed. For example, GWAS results obtained from multilocation studies related to the identification of QTLs for yield performance showed different responses, and QTLs for yield components were identified in different parts of the genome [16,17], similarly to what reported in common wheat [24,8] and barley [25,26,27]. Therefore, the success of regional projects largely relies on local GWA studies based on the evaluation of genetically diverse wild and domesticated germplasm.…”

Population Structure and Genetic Diversity of Two-Rowed Barley Accessions from Kazakhstan Based on SNP Genotyping Data

“…The SNP data for this set were acquired from the James Hutton Institute at the Germinate Barley SNP Platforms (629 accessions; https://ics.hutton.ac.uk, accessed date 16 March 2021), from Dr. T. Blake (538 accessions; Montana State University, MT, USA), from National Bioresource Project, Barley, Japan (94 accessions), and from the National Small Grains Collection (NSGC) at the USA National Plant Germplasm System (40 accessions). Except for the samples from the James Hutton Institute, most of the accessions were previously grown in Kazakhstan and analyzed using a genome-wide association study (GWAS) [3,4]. A total of 597 samples of two-rowed barley from North America (279 samples), Europe (123 samples), Western Asia (58 samples), Africa (31 samples), East Asia (9 samples), and South America (3 samples) were used.…”

Characterization of Genetic Diversity and Genome-Wide Association Mapping of Three Agronomic Traits in Qingke Barley (Hordeum Vulgare L.) in the Qinghai-Tibet Plateau

“…In earlier studies, bi-parental mapping populations were used to reliably detect QTL for HD, PH, and spike morphological traits (Lin et al, 1998 ; Sameri et al, 2006 ; Zhang et al, 2009 ). With the emergence of more cost-effective, high-throughput genotyping technologies, single nucleotide polymorphisms (SNPs) related to HD have been identified by genome-wide association studies (GWAS) (Pasam et al, 2012 ; Visioni et al, 2013 ; Genievskaya et al, 2018 ), PH (Alqudah et al, 2016 ; Almerekova et al, 2019 ), leaf area (Alqudah et al, 2018 ), spike architecture (Comadran et al, 2011 ) and grain yield (Ingvordsen et al, 2015 ; Xu et al, 2018 ) in barley. However, the genetic study of complex agronomic traits in qingke barley is limited (Zhang et al, 2019 ).…”