Marker-trait associations in two-rowed spring barley accessions from Kazakhstan and the USA

Abstract

In this study, phenotyping and single nucleotide polymorphism (SNP) genotyping data of 272 accessions of two-rowed spring barley from the USA along with 94 accessions from Kazakhstan were assessed in field trials at six breeding organizations in Kazakhstan to evaluate the performance of the USA samples over three years (2009–2011). The average grain yield over the six locations was not significantly higher in Kazakh accessions in comparison to the USA samples. Twenty four samples from Montana, Washington, the USDA station in Aberdeen Idaho, and the Anheuser-Busch breeding programs showed heavier average yield than the local standard cultivar “Ubagan”. Principal Coordinate analysis based on two sets of SNP data suggested that Kazakh accessions were closest to the USA accessions among eight groups of samples from different parts of the World, and within five US barley origin groups the samples from Montana and Washington perfectly matched six groups of Kazakh breeding origins. A genome-wide association study (GWAS) using data from eighteen field trials allowed the identification of ninety one marker-trait associations (MTA) in two or more environments for nine traits, including key characters such as heading time (HT), number of kernels per spike (NKS), and thousand grain weight (TGW). Our GWAS allowed the identification of eight MTA for HT and NKS, and sixteen MTA for TGW, when those MTA were linked to mapped SNPs. Based on comparisons of chromosomal positions of MTA identified in this study, and positions of known genes and quantitative trait loci for HT, NKS and TGW, it was suggested that MTA for HT on chromosome 2H (at 158.2 cM, 11_21414), MTA for NKS on 5H (at 118.6 cM, 11_20298), and two MTA for TGW on chromosome 4H (at 94.7 cM, 12_30718, and at 129.3 cM, 11_20013) were potentially new associations in barley. GWAS suggested that six MTA for HT, including two on chromosome 1H, two on chromosome 3H, and one each on chromosomes 4H and 6H, had useful pleiotropic effects for improving barley spike traits.

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

“…One QTL with pleotropic effects located at 91,078,604 bp on chromosome 1H was associated with all three traits in four trials. A QTL at 766,144,076 bp on chromosome 2H was related to the three traits HD_LS, PH_NM, and SL_NC, and was also associated with PH, days to seed maturation (SMT), peduncle length (PL), and HD, as reported by Genievskaya et al ( 2018 ). Of 28 pleotropic-effect QTLs, six were detected by EigenGWAS as well, and these are shown in red text highlighted in yellow in Figures 3A–C and Table 2 .…”

“…At present, the genetic architecture of grain starch quality (Li et al, 2014 ) and drought stress tolerance (Zeng et al, 2016 ) has been studied in qingke barley, and salt and aluminum tolerance have been studied in Tibetan wild barley (Qiu et al, 2011 ; Wu et al, 2011 ; Cai et al, 2013 ). In other studies, diverse barley lines from different regions, including the US (Zhou and Steffenson, 2013 ; Genievskaya et al, 2018 ), Europe (Xu et al, 2018 ), and India (Visioni et al, 2018 ), were used to identify the genetic architecture of complex traits (heading time, number of kernels per spike, grain yield) and disease resistance (durable spot, stripe rust) in barley. Although some studies used worldwide collections of barley germplasm, few have included barley varieties from Tibet (Pasam et al, 2012 ; Gyawali et al, 2017 ).…”

“…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 ).…”

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.…”

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

“…Currently, the efficiency of breeding programs might be improved by the application of modern genomic technologies [12, 13], such as the automated genome-wide profiling of large collections based on the use of single nucleotide polymorphism (SNP) markers [14, 15, 16]. In barley, an Illumina-based SNP genotyping platform was extensively used for both the evaluation of wild [17, 18, 19] and cultivated barley accessions [20, 21, 22, 23]. The fast generation of large amounts of SNP genotyping data was particularly successful for the genetic mapping of quantitative trait loci (QTL) of agronomic traits based on genome-wide association study (GWAS).…”