KASP mapping of QTLs for yield components using a RIL population in Basmati rice (Oryza sativa L.)

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  • Hamza Ashfaq
    Constituent College of Pakistan Institute of Engineering and Applied Science
  • Reena Rani
    Constituent College of Pakistan Institute of Engineering and Applied Sciences
  • Naila Perveen
    Constituent College of Pakistan Institute of Engineering and Applied Sciences
  • Allah Ditta Babar
    Constituent College of Pakistan Institute of Engineering and Applied Sciences
  • Umer Maqsood
    Constituent College of Pakistan Institute of Engineering and Applied Sciences
  • Katherine Steele
  • Muhammad Arif
    Constituent College of Pakistan Institute of Engineering and Applied Sciences
Super Basmati is an elite variety with extra-long grains and superior quality but its yield is severely affected by water stress. Recombinant inbred lines (RILs) developed from the cross of Super Basmati and IR55419-04 (a coarse grained variety with high yield potential) were used to identify and map yield-related quantitative trait loci (QTLs) under normal field conditions. Genotypes for 244 KASP markers were obtained from 188 F9 RILs and a linkage map constructed of 1369.4 cM, with average marker interval of 10.5 cM. Eleven agronomic traits were phenotyped in RILs and parents. Composite interval mapping and inclusive composite interval mapping model identified 21 common QTLs related to nine agronomic traits; of the QTLs identified, twelve mapped at novel positions. LOD scores ranged from 2.51 for number of filled grains (qFG1.1) to 16.8 for plant height (qPH1.1). Four major effect QTLs could explain 20% of variation related for plant height, hundred-grain weight and grain width. Alleles from IR55419-04 improved grain filling, grain weight and grain width, while alleles from Super Basmati contributed to longer grains, panicles and flag leaves. Putative candidate genes were identified for 18 yield-related QTLs. These results validate the use of KASP genotyping for QTL mapping of yield-related traits in a bi-parental segregating population. SNPs in the QTLs identified in this study can be used in marker assisted selection for yield components to improve Basmati rice.

Keywords

  • Kompetitive allele specific PCR (KASP), Quantitative trait loci (QTLs), SNP markers, Super Basmati, Yield-related traits
Original languageEnglish
Article number79
JournalEuphytica
Volume219
Issue number7
Early online date27 Jun 2023
DOIs
Publication statusPublished - Jul 2023
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