Validation of KASP assays associated with barley adaptation and productivity traits

Main Article Content


Yu. Genievskaya

Institute of plant biology and biotechnology, Almaty 050040, Kazakhstan
al-Farabi Kazakh National University, Almaty 050040, Kazakhstan

Sh. Almerekova

Institute of plant biology and biotechnology, Almaty 050040, Kazakhstan

V. Chudinov

Karabalyk Agricultural Experimental Station, Nauchnoe 110908, Kostanay region, Kazakhstan

Ye. Turuspekov

Institute of plant biology and biotechnology, Almaty 050040, Kazakhstan
 al-Farabi Kazakh National University, Almaty 050040, Kazakhstan

S. Abugalieva

Institute of plant biology and biotechnology, Almaty 050040, Kazakhstan


Barley (Hordeum vulgare L.) is an important cereal crop traditionally used in animal feed, malting, and food production. In Kazakhstan, barley is the second most cultivated cereal grain. However, despite the long history of barley cultivation in Kazakhstan, traditional breeding methods prevail here. The introduction of marker-assisted selection (MAS) in the breeding process may improve the adaptation and productivity of local cultivars, as well as help in the development of new ones. For that, validation of 23 kompetitive allele-specific PCR (KASP) assays for adaptation and productivity traits developed using previous GWAS results was performed. The collection of 35 two-rowed barley promising lines was grown at the Kazakh research institute of agriculture and plant growing (KRIAPG, Almaty region, Kazakhstan) in 2021 and studied for 5 adaptation-related (heading time, heading-maturity time, plant height, peduncle length, and spike length) and 5 productivity-related (number of kernels per spike, the weight of kernels per spike, weight of kernels per plant, thousand kernels weight, and yield per m2) traits. The same collection was genotyped using 23 KASP assays. As a result, 21 KASPs demonstrated a good level of polymorphism (MAF > 0.10 and I > 0.36) in the studied barley collection. Six KASP assays confirmed their associations with adaptation and productivity traits (P < 0.05); nine KASPs were associated with other agronomic traits (P < 0.05). Nine KASP assays were identified for adaptation traits, one assay was detected for productivity traits and six KASPs were found to be associated with both types of traits. Four KASP assays (ipbb_hv_9, ipbb_hv_101, ipbb_hv_109, and ipbb_hv_110) confirmed significant (P < 0.05) effect of shorter heading-maturity time on higher productivity traits under stress conditions of south-east Kazakhstan. Thus, in this study fifteen out of the studied twenty-one KASP assays were validated for their associations with adaptation and productivity traits and potentially can be included in the barley breeding projects.


Hordeum vulgare L., barley breeding, marker-assisted selection, yield, KASP genotyping

Article Details


Statista Portal. Available at: URL (Accessed 28.08.2022).

Agency for Strategic planning and reforms of the Republic of Kazakhstan Bureau of National statistics. Available at: URL (Accessed 28.08.2022).

Varshney, R.K., Mahendar, T., Aggarwal, R.K., Börner, A. Genic molecular markers in plants: development and applications // Genomics-assisted crop improvement. - 2007. - P. 13-29.

Abdi, S., Dwivedi, A., Kumar, S., Bhat, V. Development of EST-SSR markers in Cenchrus ciliaris and their applicability in studying the genetic diversity and cross-species transferability // Journal of Genetics. - 2019. - Vol. 98. - No. 4. - P. 1-16.

Leonova, I.N. Molekulyarnye marker: ispolzovanie v selekcii zenovyh kultur dlya identifikacii, introgressii i piramidirovaniya genov [Molecular markers: use in crop breeding for identification, introgression and gene pyramiding]. // Vavilov Journal of Genetics and Breeding.- 2014. - Vol. 17. - No 2. - P. 314-325.

Lister, D.L., Jones, H., Jones, M.K., O'Sullivan, D.M., Cockram, J. Analysis of DNA polymorphism in ancient barley herbarium material: validation of the KASP SNP genotyping platform // Taxon. - 2013. - Vol. 62. - No 4. - P. 779-789.

Mammadov, J., Aggarwal, R., Buyyarapu, R., Kumpatla, S. SNP markers and their impact on plant breeding // International journal of plant genomics. - 2012. - Vol. 2012. - P. 1-12.

Morgil, H., Can Gercek, Y., Tulum, I. Single Nucleotide Polymorphisms (SNPs) in plant genetics and breeding // The recent topics in genetic polymorphisms. - 2020. - doi:10.5772/intechopen.91886.

Czembor, J.H., Czembor, E., Suchecki, R., Watson-Haigh, N.S. Genome-Wide Association Study for Powdery Mildew and Rusts Adult Plant Resistance in European Spring Barley from Polish Gene Bank // Agronomy. - 2021. - Vol. 12. - No 1. - P. 7.

Gyawali, S., Chao, S., Vaish, S.S., Singh, S.P., Rehman, S., Vishwakarma, S.R., Verma, R. P.S. Genome wide association studies (GWAS) of spot blotch resistance at the seedling and the adult plant stages in a collection of spring barley // Molecular breeding. - 2018. - Vol. 38. - No 5. - P. 1-14.

Gyawali, S., Mamidi, S., Chao, S., Bhardwaj, S. C., Shekhawat, P.S., Selvakumar, R., et al. Genome-wide association studies revealed novel stripe rust resistance QTL in barley at seedling and adult-plant stages // Euphytica. - 2021. - Vol. 217. - №. 1. - P. 1-18.

Zhou, G., Broughton, S., Zhang, X.Q., Ma, Y., Zhou, M., Li, C. Genome-wide association mapping of acid soil resistance in barley (Hordeum vulgare L.) // Frontiers in plant science. - 2016. - Vol. 7. - P. 406.

Mwando, E., Han, Y., Angessa, T.T., Zhou, G., Hill, C.B., Zhang, X.Q., Li, C. Genome-Wide Association Study of Salinity Tolerance During Germination in Barley (Hordeum vulgare L.) // New Insights into Salinity Sensing, Signaling and Adaptation in Plants. - 2021. - Vol. 11. - P. 118.

Borrego-Benjumea, A., Carter, A., Zhu, M., Tucker, J.R., Zhou, M., Badea, A. Genome-wide association study of waterlogging tolerance in barley (Hordeum vulgare L.) under controlled field conditions // Frontiers in plant science. - 2021. - Vol. 11. - P. 1717.

Bai, Y., Zhao, X., Yao, X., Yao, Y., An, L., Li, X., et al. Genome wide association study of plant height and tiller number in hulless barley // PLoS ONE. - 2021. - Vol. 16. - No 12. - P. e0260723.

Maurer, A., Draba, V., Jiang, Y., Schnaithmann, F., Sharma, R., Schumann, E., et al. Modelling the genetic architecture of flowering time control in barley through nested association mapping // BMC genomics. - 2015. - Vol. 16. - No 1. - P. 1-12.

Xu, X., Sharma, R., Tondelli, A., Russell, J., Comadran, J., Schnaithmann, F., et al. Genome‐Wide Association Analysis of Grain Yield‐Associated Traits in a Pan‐European Barley Cultivar Collection // The plant genome. - 2018. - Vol. 11. – No. 1. - P. 170073.

Genievskaya, Y., Almerekova, S., Sariev, B., Chudinov, V., Tokhetova, L., Sereda, G., Ortaev, A., Tsygankov, V., Blake, T., Chao, S., Sato, K., Abugalieva, S., Turuspekov, Y. Marker–trait associations in two–rowed spring barley accessions from Kazakhstan and the USA // PLoS ONE. - 2018. - Vol. 3. - No 10. - P. e0205421.

Almerekova, S., Sariev, B., Abugalieva, A., Chudinov, V., Sereda, G., Tokhetova, L., Ortaev, A., Tsygankov, V., Blake, T., Chao, S., Genievskaya, Y., Abugalieva, S., Turuspekov, Y. Association mapping for agronomic traits in six–rowed spring barley from the USA harvested in Kazakhstan // PLoS ONE. - 2019. - Vol. 14. - No 8. - P. e0221064.

Szűcs, P. Blake, V.C., Bhat, P.R., Chao, S., Close, T.J., Cuesta‐Marcos, A., et al. An integrated resource for barley linkage map and malting quality QTL alignment // The Plant Genome. – 2009. - Vol. 2. - No 2. DOI: 10.3835/plantgenome2008.01.0005.

Li, M., Geng, L., Xie, S., Wu, D., Ye, L., Zhang, G. Genome-wide association study on total starch, amylose and amylopectin in barley grain reveals novel putative alleles // International journal of molecular sciences. - 2021. - Vol. 22. - No 2. - P. 553.

Majeed, U., Darwish, E., Rehman, S.U., Zhang, X. Kompetitive allele specific PCR (KASP): a singleplex genotyping platform and its application // Journal of Agricultural Science. - 2019. - Vol. 11. - No 1. - P. 11-20.

Xu, X., Mornhinweg, D., Bernardo, A., Li, G., Bian, R., Steffenson, B.J., Bai, G. Characterization of Rsg2. a3: A new greenbug resistance allele at the Rsg2 locus from wild barley (Hordeum vulgare ssp. spontaneum) // The Crop Journal. - 2022. DOI: 10.1016/j.cj.2022.01.010.

Gupta, S., Vassos, E., Sznajder, B., Fox, R., Khoo, K.H., Loughman, R., et al. A locus on barley chromosome 5H affects adult plant resistance to powdery mildew // Molecular Breeding. – 2018. - Vol. 38. - No 8. - P. 1-10.

Jost M., Singh D., Lagudah E., Park R. F., Dracatos P. Fine mapping of leaf rust resistance gene Rph13 from wild barley // Theoretical and Applied Genetics. - 2020. - Vol. 133. - No6. - P. 1887-1895.

Yan, L., Jiang, C., Cai, Y., Pan, Y., Xu, R., Luan, H., et al. Evaluating the genetic effects of seed dormancy regulatory genes Qsd1 and Qsd2 in a global collection of cultivated barley (Hordeum vulgare ssp. vulgare) with functional kompetitive allele‐specific PCR markers // Plant Breeding. - 2021. - Vol. 140. - No 5. - P. 827-834.

Cu, S.T., March, T.J., Degner, S., Eglinton, J.K. Identification of novel alleles from wild barley for the improvement of alpha‐amylase and related malt quality traits // Plant Breeding. - 2016. - Vol. 135. - No 6. - P. 663-670.

Houston, K., Russell, J., Schreiber, M., Halpin, C., Oakey, H., Washington, J. M., et al. A genome wide association scan for (1, 3; 1, 4)-β-glucan content in the grain of contemporary 2-row Spring and Winter barleys // BMC genomics. - 2014. - Vol. 15. - No 1. - P. 1-15.

Xu, Y. B. Developing marker-assisted selection strategies for breeding hybrid rice // Plant breeding reviews. - 2003. - P. 73-174.

Doyle, J.J., Doyle, J.L. A rapid DNA isolation procedure for small quantities of fresh leaf tissue // Phytochemical bulletin. - 1987. - Vol. 19. - No 1. - P. 11-15.

Riaz, A., Kanwal, F., Börner, A., Pillen, K., Dai, F., Alqudah, A. M. Advances in genomics-based breeding of barley: molecular tools and genomic databases // Agronomy. - 2021. - Vol. 11. - No 5. - P. 894.

Alqudah, A.M. Sharma, R., Pasam, R.K., Graner, A., Kilian, B., Schnurbusch, T. Genetic dissection of photoperiod response based on GWAS of pre-anthesis phase duration in spring barley // PLoS One. - 2014. - Vol. 9. - No. 11. - P. e113120.

Naurozbaeva Zh.K. Climatic features of the distribution of precipitation in the territory of southern and southeastern Kazakhstan during the warm period. // Journal of Geography and Environmental Management. - 2010. - Vol. 31. - No 2. - P. 108-113.

Bruckner, P.L., Frohberg, R C. Rate and Duration of Grain Fill in Spring Wheat 1 // Crop Science. - 1987. - Vol. 27. - No 3 - P. 451-455.

Passarella, V.S., Savin, R., Slafer, G.A. Breeding effects on sensitivity of barley grain weight and quality to events of high temperature during grain filling // Euphytica. - 2005. - Vol. 141. - No 1. - P. 41-48.