AUTHOR=Ur Rehman Shoaib , Ali Sher Muhammad , Saddique Muhammad Abu Bakar , Ali Zulfiqar , Khan Mahmood Alam , Mao Xinguo , Irshad Ahsan , Sajjad Muhammad , Ikram Rao Muhammad , Naeem Mahnoor , Jing Ruilian 

TITLE=Development and Exploitation of KASP Assays for Genes Underpinning Drought Tolerance Among Wheat Cultivars From Pakistan

JOURNAL=Frontiers in Genetics

VOLUME=12

YEAR=2021

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2021.684702

DOI=10.3389/fgene.2021.684702

ISSN=1664-8021

ABSTRACT=<p>High-throughput genotyping for functional markers offers an excellent opportunity to effectively practice marker-assisted selection (MAS) while breeding cultivars. We developed kompetitive allele-specific PCR (KASP) assays for genes conferring drought tolerance in common wheat (<italic>Triticum aestivum</italic> L.). In total, 11 KASP assays developed in this study and five already reported assays were used for their application in wheat breeding. We investigated alleles at 16 loci associated with drought tolerance among 153 Pakistani hexaploid wheat cultivars released during 1953–2016; 28 diploid wheat accessions (16 for AA and 12 for BB) and 19 tetraploid wheat (AABB) were used to study the evolutionary history of the studied genes. Superior allelic variations of the studied genes were significantly associated with higher grain yield. Favored haplotypes of <italic>TaSnRK2.3</italic>-1A, <italic>TaSnRK2.3</italic>-1B, <italic>TaSnRK2.9</italic>-5A, <italic>TaSAP</italic>-7B, and <italic>TaLTPs</italic>-1A predominated in Pakistani wheat germplasm indicating unconscious pyramiding and selection pressure on favorable haplotypes during selection breeding. <italic>TaSnRK2.8</italic>-5A, <italic>TaDreb</italic>-B1, <italic>1-feh w3</italic>, <italic>TaPPH</italic>-7A, <italic>TaMOC</italic>-7A, and <italic>TaPARG</italic>-2A had moderate to low frequencies of favorable haplotype among Pakistani wheat germplasm pointing toward introgression of favorable haplotypes by deploying functional markers in marker-assisted breeding. The KASP assays were compared with gel-based markers for reliability and phenotypically validated among 62 Pakistani wheat cultivars. Association analyses showed that the favorable allelic variations were significantly associated with grain yield-contributing traits. The developed molecular marker toolkit of the genes can be instrumental for the wheat breeding in Pakistan.</p>