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<p><i>Β-amylase</i> (<i>BAM</i>) gene family is an important genetic resource that catalyzes starch metabolism and responds positively in response to abiotic stresses. In current work, 28 <i>TaBAMs</i> were identified through genome wide analysis using AtBAM domain. Phylogenetic analysis grouped these genes into four sub-groups. Gene structure, conserved motif, <i>cis</i>-acting elements, and synteny analysis suggested evolutionary conserveness within <i>TaBAM</i> gene family. Pangenome analysis suggested that <i>TaBAMs</i> are core set of genes and are present as single copy loci. Transcriptome profiling and qRT-PCR identified <i>TaBAM16</i>-1B and <i>TaBAM20</i>-4D as drought responsive candidate genes. Sequence polymorphism analysis revealed non-synonymous (A<sup>3040</sup>/G<sup>3040</sup>) SNP site only in the coding region of <i>TaBAM16</i>-1B resulting in Cys to Tyr substitution. KASP technique was deployed to convert the identified SNPs into molecular markers. Using 183 Pakistani wheat genotypes across four environments, marker trait association studies demonstrated significant association with normalized difference vegetative index (NDVI) trait, in three out of four environments. Enzymatic activity analysis confirmed that <i>TaBAM16</i>-1B Allele-A (superior allele) carrying varieties maintained stable <i>β-amylase</i> activity under PEG-induced drought condition, especially in roots at 24-h time interval. <i>TaBAM16</i>-1B EMS mutants provided genetic validation revealing reduced total chlorophyll contents under drought stress. Allelic variations of <i>TaBAM16</i>-1B were also explored in 299 global wheat germplasm collected from 19 countries. <i>TaBAM16</i>-1B Allele-A has been positively selected in drought prone areas underscoring selection pressure exerted by the wheat breeders. Current work identifies <i>TaBAM16</i>-1B as a functional gene and offers a KASP marker for marker-assisted wheat breeding to improve the drought tolerance.</p>

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Pangenome-assisted characterization of TaBAM genes and association of TaBAM16-1B with NDVI in wheat

  • 期刊论文

  • 发表日期：

    2026年4月25日

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  • Maira Anam,
  • Zulqurnain Khan,
  • Muhammad Ali Sher,
  • Muhammad Sajjad,
  • Muhammad Kashif Naeem,
  • Zijin Zhang,
  • Sania Javeed,
  • Fatima Javeria,
  • Jing Chen,
  • Shoaib Ur Rehman

摘要

Β-amylase (BAM) gene family is an important genetic resource that catalyzes starch metabolism and responds positively in response to abiotic stresses. In current work, 28 TaBAMs were identified through genome wide analysis using AtBAM domain. Phylogenetic analysis grouped these genes into four sub-groups. Gene structure, conserved motif, cis-acting elements, and synteny analysis suggested evolutionary conserveness within TaBAM gene family. Pangenome analysis suggested that TaBAMs are core set of genes and are present as single copy loci. Transcriptome profiling and qRT-PCR identified TaBAM16-1B and TaBAM20-4D as drought responsive candidate genes. Sequence polymorphism analysis revealed non-synonymous (A3040/G3040) SNP site only in the coding region of TaBAM16-1B resulting in Cys to Tyr substitution. KASP technique was deployed to convert the identified SNPs into molecular markers. Using 183 Pakistani wheat genotypes across four environments, marker trait association studies demonstrated significant association with normalized difference vegetative index (NDVI) trait, in three out of four environments. Enzymatic activity analysis confirmed that TaBAM16-1B Allele-A (superior allele) carrying varieties maintained stable β-amylase activity under PEG-induced drought condition, especially in roots at 24-h time interval. TaBAM16-1B EMS mutants provided genetic validation revealing reduced total chlorophyll contents under drought stress. Allelic variations of TaBAM16-1B were also explored in 299 global wheat germplasm collected from 19 countries. TaBAM16-1B Allele-A has been positively selected in drought prone areas underscoring selection pressure exerted by the wheat breeders. Current work identifies TaBAM16-1B as a functional gene and offers a KASP marker for marker-assisted wheat breeding to improve the drought tolerance.