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<p>The&#xa0;eating and cooking quality of rice varieties should not compromised during breeding for future growing conditions in all rice growing countries. As a case study, KASP markers for genes related to starch and aroma traits were tested for their association with amylose content (AC) and alkaline spreading value (ASV) in thirty-two rice varieties from Pakistan representing diversity in both traits. Seventeen KASP revealed variants among Pakistani varieties: SNPs in six starch-related genes and an InDel in the fragrance gene <i>BADH2</i>. All Pakistani varieties had the <i>Wx</i><sup><i>a</i></sup> allele of the <i>Waxy</i> gene (<i>OsGBSSI</i>) and none possessed low-AC alleles: <i>wx</i>, <i>Wx</i><sup><i>mq</i></sup> or <i>Wx</i><sup><i>op</i></sup>. Population structure analysis of marker&#xa0;data indicated four ancestorial subgroups among the&#xa0;Pakistani genotypes: Japonica, Basmati, low-ASV Indica and high-ASV indica. Varieties with alleles for ‘low’ and intermediate’ AC tended to have alleles for ‘lower’ ASV. Fragrance and AC were correlated (r = 0.608) with non-aromatic varieties having 25.4%&#xa0;mean AC and aromatic varieties having 21.9%&#xa0;mean&#xa0;AC. Most non-aromatic varieties had the <i>alk</i><sup><i>j</i></sup> allele of the <i>OsSSII_a/SSII_3</i> (<i>Alk</i>) gene and most aromatic varieties had <i>alk</i><sup><i>i</i></sup>. Functional SNPs in <i>Alk</i>, <i>BADH2,</i> and <i>PPR</i> genes were associated with ASV, and a functional SNP in <i>OsSSII_b</i> was associated with AC and ASV. Three exonic <i>Waxy</i> loci were correlated with both AC and ASV while four non-functional KASP were in linkage disequilibrium with these alleles. These findings indicate that KASP could inform selection of eating and cooking quality in appropriate crosses.</p>

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Association of KASP with starch-trait diversity in modern rice grown in Pakistan

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  • 发表日期：

    2025年6月18日

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  • Kamran Yaqoob,
  • Saddia Galani,
  • Kazim Ali,
  • Rolf Kraehenbuehl,
  • Katherine A. Steele

摘要

The eating and cooking quality of rice varieties should not compromised during breeding for future growing conditions in all rice growing countries. As a case study, KASP markers for genes related to starch and aroma traits were tested for their association with amylose content (AC) and alkaline spreading value (ASV) in thirty-two rice varieties from Pakistan representing diversity in both traits. Seventeen KASP revealed variants among Pakistani varieties: SNPs in six starch-related genes and an InDel in the fragrance gene BADH2. All Pakistani varieties had the Wxa allele of the Waxy gene (OsGBSSI) and none possessed low-AC alleles: wx, Wxmq or Wxop. Population structure analysis of marker data indicated four ancestorial subgroups among the Pakistani genotypes: Japonica, Basmati, low-ASV Indica and high-ASV indica. Varieties with alleles for ‘low’ and intermediate’ AC tended to have alleles for ‘lower’ ASV. Fragrance and AC were correlated (r = 0.608) with non-aromatic varieties having 25.4% mean AC and aromatic varieties having 21.9% mean AC. Most non-aromatic varieties had the alkj allele of the OsSSII_a/SSII_3 (Alk) gene and most aromatic varieties had alki. Functional SNPs in Alk, BADH2, and PPR genes were associated with ASV, and a functional SNP in OsSSII_b was associated with AC and ASV. Three exonic Waxy loci were correlated with both AC and ASV while four non-functional KASP were in linkage disequilibrium with these alleles. These findings indicate that KASP could inform selection of eating and cooking quality in appropriate crosses.