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

Date Published: October 11, 2018

Publisher: Public Library of Science

Author(s): Yuliya Genievskaya, Shyryn Almerekova, Burabai Sariev, Vladimir Chudinov, Laura Tokhetova, Grigoriy Sereda, Anarbai Ortaev, Vladimir Tsygankov, Thomas Blake, Shiaoman Chao, Kazuhiro Sato, Saule Abugalieva, Yerlan Turuspekov, Dragan Perovic.


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.

Partial Text

Barley (Hordeum vulgare L. spp vulgare) is an important crop in the agricultural sector of Kazakhstan, and it is grown in many different climatic zones over 1.5 million hectares annually. Currently, it is the second most widely-grown cereal crop in the country after wheat with on average an annual total grain yield of 2.0 million tons [1]. The end use for barley in the country is animal feed, and the average yield is 1.5 ton per hectare [1]. Traditionally, two-rowed spring barley is the dominant type in all major barley growing regions as the country has long and cold winters and often arid summers. The summertime is stressful in two out of three years due to drought and heat causing substantial grain yield loss [1].

The performance of the USA barley accessions in field trials in six different regions of Kazakhstan was high as their average yield was not significantly less than the average yield of local accessions. In particular, the study allowed the identification of several accessions from MT, WA, AB, and BA, which outperformed the local standard cultivar in Northern Kazakhstan, where more than 90% of the barley acreage is planted. The variation in grain yield can be explained by the sensitivity of genotypes to environmental factors at crucial growth phases such as flowering time [31]. Therefore, the application of molecular markers in understanding genotype-environment interactions, and their use in early stages in breeding projects can be very efficient [59]. In this study GWAS suggested that six MTA for HT, including two on chromosome 1H, two on chromosome 3H, and one each on chromosomes 4H and 6H, have large pleiotropic effects and could be useful for improving barley grain yield potential. It is interesting that two MTA for HT on 1H (11_11336 and 11_10176) were matched the positions of genes HvCMF10 and HvCMF11, and one of the two MTA on 3H (11_10935) was mapped in close vicinity to HvLUX [48]. The MTA on 4H (11_21303) is located close to the HvCO16/HvPRR59/HVPRR73 genes, and the MTA on 6H is coincident with the location of the HvCO5/HvPRR1/HvTOC1 gene cluster reported in Alqudah et al., 2014 [48]. However, the remaining MTA on 3H (11_21505) did not match the locations of any previously known major flowering genes. In addition, the MTA for HT on chromosome 2H (at 158.2 cM, 12_21414) was presumably novel association in barley identified in this study. As the effects of climate change become more obvious, international exchange and evaluation of germplasm will help ameliorate the yield penalties that local environmental changes exact.




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