Dataset Information

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.

SUBMITTER: Almerekova S

PROVIDER: S-EPMC6690582 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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

Almerekova Shyryn S Sariev Burabai B Abugalieva Aigul A Chudinov Vladimir V Sereda Grigoriy G Tokhetova Laura L Ortaev Anarbai A Tsygankov Vladimir V Blake Thomas T Chao Shiaoman S Genievskaya Yuliya Y Abugalieva Saule S Turuspekov Yerlan Y

PloS one 20190812 8

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 polymor ...[more]

PMID: 31404111

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Project description: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.

Project description:In recent years soybean is becoming one of the most important oilseed crops in Kazakhstan. Only within the last ten years (2006-2016), the area under soybean is expanded from 45 thousand hectares (ha) in 2006 to 120 thousand ha in 2016. The general trend of soybean expansion is from south-eastern to eastern and northern regions of the country, where average temperatures are lower and growing seasons are shorter. These new soybean growing territories were poorly examined in terms of general effects on productivity level among the diverse sample of soybean accessions. In this study, phenotypic data were collected in three separate regions of Kazakhstan and entire soybean sample was genotyped for identification of marker-trait associations (MTA).In this study, the collection of 113 accessions representing five different regions of the World was planted in 2015-2016 in northern, eastern, and south-eastern regions of Kazakhstan. It was observed that North American accessions showed the highest yield in four out of six trials especially in Northern Kazakhstan in both years. The entire sample was genotyped with 6 K SNP Illumina array. 4442 SNPs found to be polymorphic and were used for whole genome genotyping purposes. Obtained SNP markers data and field data were used for GWAS (genome-wide association study). 30 SNPs appear to be very significant in 42 MTAs in six studied environments.The study confirms the efficiency of GWAS for the identification of molecular markers which tag important agronomic traits. Overall thirty SNP markers associated with time to flowering and maturation, plant height, number of fertile nodes, seeds per plant and yield were identified. Physical locations of 32 identified out of 42 total MTAs coincide well with positions of known analogous QTLs. This result indicates importance of revealed MTAs for soybean growing regions in Kazakhstan. Obtained results would serve as required prerequisite for forming and realization of specific breeding programs towards effective adaptation and increased productivity of soybean in three different regions of Kazakhstan.

Project description:We recently reported three earliness per se quantitative trait loci (QTL) associated with flowering and maturity in a recombinant inbred lines (RILs) population derived from a cross between the spring wheat (Triticum aestivum L.) cultivars 'Cutler' and 'AC Barrie' using 488 microsatellite and diversity arrays technology (DArT) markers. Here, we present QTLs associated with flowering time, maturity, plant height, and grain yield using high density single nucleotide polymorphic (SNP) markers in the same population. A mapping population of 158 RILs and the two parents were evaluated at five environments for flowering, maturity, plant height and grain yield under field conditions, at two greenhouse environments for flowering, and genotyped with a subset of 1809 SNPs out of the 90K SNP array and 2 functional markers (Ppd-D1 and Rht-D1). Using composite interval mapping on the combined phenotype data across all environments, we identified a total of 19 QTLs associated with flowering time in greenhouse (5), and field (6) conditions, maturity (5), grain yield (2) and plant height (1). We mapped these QTLs on 8 chromosomes and they individually explained between 6.3 and 37.8% of the phenotypic variation. Four of the 19 QTLs were associated with multiple traits, including a QTL on 2D associated with flowering, maturity and grain yield; two QTLs on 4A and 7A associated with flowering and maturity, and another QTL on 4D associated with maturity and plant height. However, only the QTLs on both 2D and 4D had major effects, and they mapped adjacent to well-known photoperiod response Ppd-D1 and height reducing Rht-D1 genes, respectively. The QTL on 2D reduced flowering and maturity time up to 5 days with a yield penalty of 436 kg ha-1, while the QTL on 4D reduced plant height by 13 cm, but increased maturity by 2 days. The high density SNPs allowed us to map eight moderate effect, two major effect, and nine minor effect QTLs that were not identified in our previous study using microsatellite and DArT markers. Results from this study provide additional information to wheat researchers developing early maturing and short stature spring wheat cultivars.

Dataset Information

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

Publications

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

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