Identification of Wheat Septoria tritici Resistance Genes in Wheat Germplasm Using Molecular Markers.

Zymoseptoria tritici (Z. tritici) is the main threat to global food security; it is a fungal disease that presents one of the most serious threats to wheat crops, causing severe yield losses worldwide, including in Kazakhstan. The pathogen leads to crop losses reaching from 15 to 50%. The objectives of this study were to (1) evaluate a wheat collection for Z. tritici resistance during the adult plant and seedling growth stages, (2) identify the sources of resistance genes that provide resistance to Z. tritici using molecular markers linked to Stb genes, and (3) identify potentially useful resistant wheat genotypes among cultivars and advanced breeding lines. This study evaluated 60 winter and spring wheat genotypes for Z. tritici resistance. According to the field reactions, 22 entries (35.7%) showed ≤10% disease severity in both years. The resistant reaction to a mix of Z. tritici isolates in the seedling stage was associated with adult plant resistance to disease in four wheat entries. The resistance of Rosinka 3 was due to the presence of Stb8; Omskaya 18 showed an immune reaction in the field and a moderately susceptible reaction in the seedling stage, possibly provided by a combination of the Stb7 and Stb2 genes. The high resistance in both the adult and seedling stages of Omskaya 29 and KR11-03 was due to the Stb4 and Stb2 genes and, possibly, due to the presence of unknown genes. A linked marker analysis revealed the presence of several Stb genes. The proportion of wheat entries with Stb genes was quite high at twenty-seven of the genotypes tested (45.0%), including four from Kazakhstan, nine from Russia, nine from the CIMMYT-ICARDA-IWWIP program, and five from the CIMMYT-SEPTMON nursery. Among the sixty entries, ten (16.7%) carried the resistance genes Stb2 and Stb8, and the gene Stb4 was found in seven cultivars (11.6%). Marker-assisted selection can be efficiently applied to develop wheat cultivars with effective Stb gene combinations that would directly assist in developing durable resistance in Kazakhstan. Resistant genotypes could also be used as improved parents in crossing programs to develop new wheat cultivars.

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

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.

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

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.