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Background <p><i>Arachis monticola</i> (<i>A.mon</i>), an allotetraploid wild species, regarded as the direct ancestor of cultivated peanut <i>Arachis hypogaea</i> (<i>A.hypogaea</i>) during the evolution of the <i>Arachis</i> genus, exhibits significantly different agronomic traits from that of its allotetraploid cultivated relative, such as special fruit structure, small pods and seeds. However, the molecular mechanisms underlying these genetic variations remain unclear.</p> Results <p>In this study, using the tandem mass tags (TMT) strategy, we performed quantitative proteomic analysis of the developing seeds at early (S2) and late (S4) stages from <i>A.mon</i> and two cultivated peanut accessions (L8106 and L8107), and identified differentially expressed proteins (DEPs) among these samples. <i>A.mon</i> had a significantly lower 100-seed weight than that of both L8106 and L8107, which was mainly attributed to the dramatically reduced cell number and smaller cell width in seeds. We presented a quantitative proteome map consisting of 8,762 proteins in developing seeds from wild as well as cultivated peanuts. In comparison with <i>A.mon</i>, a total of 297 (133 up-regulated, 164 down- regulated) and 306 (95 up-regulated and 211 down-regulated) shared DEPs were identified in both cultivated accessions at S2 and S4, respectively. Among those up-regulated proteins, the pathways “nitrogen metabolism” and “carbon fixation” were simultaneously enriched at both stages, while the pathway “diterpenoid biosynthesis” was concurrently overrepresented in those down-regulated proteins. Notably, peanut fructose-bisphosphate aldolase 3 (AhFBA3), jointly enriched in both the pathways nitrogen metabolism and carbon metabolism, showed substantially increased protein abundance by ≥ 4 times in seeds of both cultivated lines compared to <i>A.mon</i>. More importantly, by genotyping 194 peanut accessions, two haplotypes based on a C-to-T change at nucleotide 2165 of <i>AhFBA3</i>, were generated. Peanut accessions carrying <i>Hap_T</i> showed significantly increased 100-seed weight than those carrying <i>Hap_C</i>. Additionally, 69.70% carreid the haplotype <i>Hap_T</i> among the subspecies <i>hypogaea</i> accessions with big seeds, while the majority (94.50%) of the subspecies <i>fastigiata</i> with small seeds had the haplotype <i>Hap_C.</i> Therefore, these results collectively indicated that <i>AhFBA3</i> influenced peanut seed weight.</p> Conclusions <p>Our findings help to understand the molecular mechanisms underlying seed trait variation during peanut domestication, and provide key candidate proteins (genes) and superior haplotype for breeding high-yield peanut cultivars.</p>

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Comparative proteomics analysis of wild and cultivated accessions reveals key candidate proteins associated with seed weight variations in peanut

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  • 发表日期：

    2026年4月20日

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  • Zhongfeng Li,
  • Zenghui Cao,
  • Kai Zhao,
  • Fangping Gong,
  • Ding Qiu,
  • Rui Ren,
  • Kunkun Zhao,
  • Xingli Ma,
  • Dongmei Yin

摘要

Background

Arachis monticola (A.mon), an allotetraploid wild species, regarded as the direct ancestor of cultivated peanut Arachis hypogaea (A.hypogaea) during the evolution of the Arachis genus, exhibits significantly different agronomic traits from that of its allotetraploid cultivated relative, such as special fruit structure, small pods and seeds. However, the molecular mechanisms underlying these genetic variations remain unclear.

Results

In this study, using the tandem mass tags (TMT) strategy, we performed quantitative proteomic analysis of the developing seeds at early (S2) and late (S4) stages from A.mon and two cultivated peanut accessions (L8106 and L8107), and identified differentially expressed proteins (DEPs) among these samples. A.mon had a significantly lower 100-seed weight than that of both L8106 and L8107, which was mainly attributed to the dramatically reduced cell number and smaller cell width in seeds. We presented a quantitative proteome map consisting of 8,762 proteins in developing seeds from wild as well as cultivated peanuts. In comparison with A.mon, a total of 297 (133 up-regulated, 164 down- regulated) and 306 (95 up-regulated and 211 down-regulated) shared DEPs were identified in both cultivated accessions at S2 and S4, respectively. Among those up-regulated proteins, the pathways “nitrogen metabolism” and “carbon fixation” were simultaneously enriched at both stages, while the pathway “diterpenoid biosynthesis” was concurrently overrepresented in those down-regulated proteins. Notably, peanut fructose-bisphosphate aldolase 3 (AhFBA3), jointly enriched in both the pathways nitrogen metabolism and carbon metabolism, showed substantially increased protein abundance by ≥ 4 times in seeds of both cultivated lines compared to A.mon. More importantly, by genotyping 194 peanut accessions, two haplotypes based on a C-to-T change at nucleotide 2165 of AhFBA3, were generated. Peanut accessions carrying Hap_T showed significantly increased 100-seed weight than those carrying Hap_C. Additionally, 69.70% carreid the haplotype Hap_T among the subspecies hypogaea accessions with big seeds, while the majority (94.50%) of the subspecies fastigiata with small seeds had the haplotype Hap_C. Therefore, these results collectively indicated that AhFBA3 influenced peanut seed weight.

Conclusions

Our findings help to understand the molecular mechanisms underlying seed trait variation during peanut domestication, and provide key candidate proteins (genes) and superior haplotype for breeding high-yield peanut cultivars.