Teosinte confers specific alleles and yield potential to maize improvement

Wang, Qingjun; Liao, Zhengqiao; Zhu, Chenfeng; Gou, Xiangjian; Liu, Yaxi; Xie, Wubing; Wu, Fengkai; Feng, Xin; Xu, Jie; Li, Jingwei; Lu, Yanli

doi:10.1007/s00122-022-04199-5

Cited by 11 publications

(9 citation statements)

References 62 publications

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“…The filtered SNPs were genotyped based on the following criteria: (1) Homozygous for each mapping parent and different between two parents; (2) Bi-allelic polymorphism among the F 2 individuals; (3) The missing rate were no more than 5%; (4) The extreme segregation distorted SNPs were excluded at the cut-off (P [?] 1×10 7 ) in the separation of Mendelian law (Zhanget al ., 2010;Zuo et al ., 2019;Wang et al ., 2022). Finally, we obtained 38,144 SNPs in total.…”

Section: Sequencing and Genotypingmentioning

confidence: 99%

Genetic architecture of ecological divergence between two wild rice species (Oryza rufipogon and O. nivara)

Meng,

Chenggen,

et al. 2023

Preprint

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Ecological divergence due to habitat difference plays a prominent role in the formation of new species but the genetic architecture during ecological speciation and the mechanism underlying phenotypic divergence remain less understood. Two wild rice species (O. rufipogon and O. nivara) are a progenitor-derivative species pair with ecological divergence and provide a unique system for studying ecological adaptation/speciation. Here, we constructed a high-resolved linkage map and conducted a quantitative trait locus (QTL) analysis of 19 phenotypic traits using an F2 population generated from a cross between the two wild rice species. We identified 113 QTLs associated with interspecific divergence of 16 quantitative traits, with effect sizes ranging from 1.61% to 34.1% in terms of the percentage of variation explained (PVE). The distribution of effect sizes of QTLs followed a negative exponential, suggesting that a few genes of large effect and many genes of small effect were responsible for the phenotypic divergence. We observed 18 clusters of QTLs (QTL hotspots) on 11 chromosomes, significantly more than that expected by chance, demonstrating the importance of coinheritance of loci/genes in ecological adaptation/speciation. Analysis of effect direction and v-test statistics revealed that interspecific differentiation of most traits was driven by divergent natural selection, supporting the argument that ecological adaptation/speciation would proceed rapidly under coordinated selection on multiple traits. Our findings provide new insights into the understanding of genetic architecture of ecological adaptation and speciation in plants and helps effective manipulation of specific genes or gene cluster in rice breeding.

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Section: Sequencing and Genotypingmentioning

confidence: 99%

Genetic architecture of ecological divergence between two wild rice species (Oryza rufipogon and O. nivara)

Meng,

Chenggen,

et al. 2023

Preprint

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“…Teosinte possesses abundant genetic diversity and numerous beneficial genes with substantial breeding value. Favorable alleles in teosinte are domesticated into specific alleles in different subgroups through gene infiltration and artificial selection, laying the foundation for heterosis formation [ 8 , 55 , 64 , 65 ]. Our analysis demonstrated the significant enrichment of 758 ASEGs in regions associated with heterosis-related genes, with 10 heterosis-related BS ASEGs being significantly domesticated (Fig.…”

Section: Discussionmentioning

confidence: 99%

Natural variations of heterosis-related allele-specific expression genes in promoter regions lead to allele-specific expression in maize

Zhan,

Cui,

Yang

et al. 2024

BMC Genomics

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Background Heterosis has successfully enhanced maize productivity and quality. Although significant progress has been made in delineating the genetic basis of heterosis, the molecular mechanisms underlying its genetic components remain less explored. Allele-specific expression (ASE), the imbalanced expression between two parental alleles in hybrids, is increasingly being recognized as a factor contributing to heterosis. ASE is a complex process regulated by both epigenetic and genetic variations in response to developmental and environmental conditions. Results In this study, we explored the differential characteristics of ASE by analyzing the transcriptome data of two maize hybrids and their parents under four light conditions. On the basis of allele expression patterns in different hybrids under various conditions, ASE genes were divided into three categories: bias-consistent genes involved in basal metabolic processes in a functionally complementary manner, bias-reversal genes adapting to the light environment, and bias-specific genes maintaining cell homeostasis. We observed that 758 ASE genes (ASEGs) were significantly overlapped with heterosis quantitative trait loci (QTLs), and high-frequency variations in the promoter regions of heterosis-related ASEGs were identified between parents. In addition, 10 heterosis-related ASEGs participating in yield heterosis were selected during domestication. Conclusions The comprehensive analysis of ASEGs offers a distinctive perspective on how light quality influences gene expression patterns and gene-environment interactions, with implications for the identification of heterosis-related ASEGs to enhance maize yield.

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“…The filtered SNPs were genotyped based on the following criteria: (1) homozygous for each mapping parent and different between two parents; (2) bi‐allelic polymorphism among the F 2 individuals; (3) the missing rates were no more than 5%; (4) the extreme segregation distorted SNPs were excluded at the cut‐off ( P ≤ 1 × 10 −7 ) in the separation of Mendelian law (Wang et al., 2022; Zhang et al., 2010; Zuo et al., 2019). Finally, we obtained 38,144 SNPs in total.…”

Section: Methodsmentioning

confidence: 99%

“…Variant calling was conducted using the Genome Analysis Toolkit (GATK, version 4.0. (3) the missing rates were no more than 5%; (4) the extreme segregation distorted SNPs were excluded at the cut-off (P ≤ 1 × 10 −7 ) in the separation of Mendelian law (Wang et al, 2022;Zhang et al, 2010;Zuo et al, 2019). Finally, we obtained 38,144 SNPs in total.…”

Section: Sequencing and Genotypingmentioning

confidence: 99%

Genetic architecture of ecological divergence between Oryza rufipogon and Oryza nivara

Meng,

Qiang,

et al. 2024

Molecular Ecology

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Ecological divergence due to habitat difference plays a prominent role in the formation of new species, but the genetic architecture during ecological speciation and the mechanism underlying phenotypic divergence remain less understood. Two wild ancestors of rice (Oryza rufipogon and Oryza nivara) are a progenitor‐derivative species pair with ecological divergence and provide a unique system for studying ecological adaptation/speciation. Here, we constructed a high‐resolution linkage map and conducted a quantitative trait locus (QTL) analysis of 19 phenotypic traits using an F2 population generated from a cross between the two Oryza species. We identified 113 QTLs associated with interspecific divergence of 16 quantitative traits, with effect sizes ranging from 1.61% to 34.1% in terms of the percentage of variation explained (PVE). The distribution of effect sizes of QTLs followed a negative exponential, suggesting that a few genes of large effect and many genes of small effect were responsible for the phenotypic divergence. We observed 18 clusters of QTLs (QTL hotspots) on 11 chromosomes, significantly more than that expected by chance, demonstrating the importance of coinheritance of loci/genes in ecological adaptation/speciation. Analysis of effect direction and v‐test statistics revealed that interspecific differentiation of most traits was driven by divergent natural selection, supporting the argument that ecological adaptation/speciation would proceed rapidly under coordinated selection on multiple traits. Our findings provide new insights into the understanding of genetic architecture of ecological adaptation and speciation in plants and help effective manipulation of specific genes or gene cluster in rice breeding.

show abstract

Teosinte confers specific alleles and yield potential to maize improvement

Cited by 11 publications

References 62 publications

Genetic architecture of ecological divergence between two wild rice species (Oryza rufipogon and O. nivara)

Genetic architecture of ecological divergence between two wild rice species (Oryza rufipogon and O. nivara)

Natural variations of heterosis-related allele-specific expression genes in promoter regions lead to allele-specific expression in maize

Genetic architecture of ecological divergence between Oryza rufipogon and Oryza nivara

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