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Key message <p>Critical genes underlying variations in photosynthetic pigments and productivity-related traits were identified. We also identified 88 zones of collinearity in the A-genomes of B. juncea and B. napus, which harboured the same photosynthetic genes.</p> Abstract <p>Chlorophylls and carotenoids are essential for photosynthesis, phenotypic plasticity, and environmental resilience in plants, but the natural variation of these pigments has largely remained underexplored and underutilized. We employed a forward genetics approach on 286 genotypes of mustard (<i>Brassica juncea</i> (L.) Czern), a crop known for its oil, condiments, and vegetables, to identify the genes responsible for variation for these traits. The test genotypes were evaluated in three environments that varied in sunlight hours, irradiance, and temperatures during the vegetative and early pod formation stages of the crop. The studies revealed a wide but continuous variation with strong genotype-environment interactions. A genome-wide association study (GWAS) found 507 marker trait associations (MTAs) for photosynthesis pigments, 28 for seed yield, and 83 for oil content. The annotation of 150&#xa0;kb of genome space around associated SNPs facilitated the prediction of 88 candidate genes; 28 of these were projected repeatedly over the traits and environments, 15 of these could be validated through associative transcriptomics. Prediction of candidate genes with roles in minimizing excess energy dissipation (<i>DAL1</i>),&#xa0;adjusting chlorophyll b levels (<i>IM</i>, <i>CGA1</i>), or regulating antenna size (<i>AT3G56290</i>) was especially important. We also catalogued cis-regulatory elements such as <i>G-box</i>, <i>circadian elements</i>, <i>HD-Zip-1</i> binding sites, and various light-responsive motifs for several candidate genes. Synteny and evolutionary analyses based on the predicted genes identified 88 zones of collinearity with the <i>Brassica napus</i>—A genome, including genes related to photosynthetic pigments, which could be useful for improving photosynthetic efficiency through plant breeding and bioengineering methods.</p>

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Genetic basis of natural variation for photosynthetic pigments in Brassica juncea leaves and silique walls under differing photoperiod conditions

  • 期刊论文

  • 发表日期：

    2026年4月15日

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  • Aaftab Alam Ansari,
  • Sanjula Sharma,
  • Javed Akhatar,
  • Harjeevan Kaur,
  • Surinder S. Banga,
  • Chhaya Atri

摘要

Key message

Critical genes underlying variations in photosynthetic pigments and productivity-related traits were identified. We also identified 88 zones of collinearity in the A-genomes of B. juncea and B. napus, which harboured the same photosynthetic genes.

Abstract

Chlorophylls and carotenoids are essential for photosynthesis, phenotypic plasticity, and environmental resilience in plants, but the natural variation of these pigments has largely remained underexplored and underutilized. We employed a forward genetics approach on 286 genotypes of mustard (Brassica juncea (L.) Czern), a crop known for its oil, condiments, and vegetables, to identify the genes responsible for variation for these traits. The test genotypes were evaluated in three environments that varied in sunlight hours, irradiance, and temperatures during the vegetative and early pod formation stages of the crop. The studies revealed a wide but continuous variation with strong genotype-environment interactions. A genome-wide association study (GWAS) found 507 marker trait associations (MTAs) for photosynthesis pigments, 28 for seed yield, and 83 for oil content. The annotation of 150 kb of genome space around associated SNPs facilitated the prediction of 88 candidate genes; 28 of these were projected repeatedly over the traits and environments, 15 of these could be validated through associative transcriptomics. Prediction of candidate genes with roles in minimizing excess energy dissipation (DAL1), adjusting chlorophyll b levels (IM, CGA1), or regulating antenna size (AT3G56290) was especially important. We also catalogued cis-regulatory elements such as G-box, circadian elements, HD-Zip-1 binding sites, and various light-responsive motifs for several candidate genes. Synteny and evolutionary analyses based on the predicted genes identified 88 zones of collinearity with the Brassica napus—A genome, including genes related to photosynthetic pigments, which could be useful for improving photosynthetic efficiency through plant breeding and bioengineering methods.