Population-scale gene expression analysis reveals the contribution of expression diversity to the modern wheat improvement DOI Open Access
Zhimeng Zhang, Shengwei Ma,

Mou Yin

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2025, Номер unknown

Опубликована: Фев. 23, 2025

Abstract Changes in gene expression are crucial for crop breeding, yet population genomics has primarily focused on sequence polymorphisms rather than diversity. The strategy of using single genome reference RNA-seq analysis could not handle introgression bias, especially hexaploidy wheat. Here, we conducted 328 wheat lines, including representative diverse landraces and elite cultivars from China the United States, to investigate role variation shaping agronomic traits. Using pan-genome resources, identified 20,615 more transcripts ‘Chinese Spring’ alone. We constructed a pan-gene atlas regulatory map through eQTL analysis, demonstrating that genes introgressed wild relatives were under tight genetic control. Genes responding environmental stress show higher activity after into genome, how long-term breeding selection impacted regulation targeted introgression. Multi-omics modeling 231 high-confidence candidate 34 field traits seedling resistance phenotypes 8 powdery mildew isolates. More one fifth those candidates have no homolog genome. By utilizing indexed KN9204 EMS library, 80% showed significant trait difference between type mutant lines. Furthermore, directional shifts which changed by improvement demonstrated distinct adaptations local environments. Our study correct bias reads mapping studies revealed patterns within their mechanisms, highlighted impact world’s most important crop.

Язык: Английский

Population-scale gene expression analysis reveals the contribution of expression diversity to the modern wheat improvement DOI Open Access
Zhimeng Zhang, Shengwei Ma,

Mou Yin

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2025, Номер unknown

Опубликована: Фев. 23, 2025

Abstract Changes in gene expression are crucial for crop breeding, yet population genomics has primarily focused on sequence polymorphisms rather than diversity. The strategy of using single genome reference RNA-seq analysis could not handle introgression bias, especially hexaploidy wheat. Here, we conducted 328 wheat lines, including representative diverse landraces and elite cultivars from China the United States, to investigate role variation shaping agronomic traits. Using pan-genome resources, identified 20,615 more transcripts ‘Chinese Spring’ alone. We constructed a pan-gene atlas regulatory map through eQTL analysis, demonstrating that genes introgressed wild relatives were under tight genetic control. Genes responding environmental stress show higher activity after into genome, how long-term breeding selection impacted regulation targeted introgression. Multi-omics modeling 231 high-confidence candidate 34 field traits seedling resistance phenotypes 8 powdery mildew isolates. More one fifth those candidates have no homolog genome. By utilizing indexed KN9204 EMS library, 80% showed significant trait difference between type mutant lines. Furthermore, directional shifts which changed by improvement demonstrated distinct adaptations local environments. Our study correct bias reads mapping studies revealed patterns within their mechanisms, highlighted impact world’s most important crop.

Язык: Английский

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