Genetic and Geographic Patterns of Duplicate DPL Genes Causing Genetic Incompatibility Within Rice: Implications for Multiple Domestication Events in Rice

Xu, Xun; Ge, Song; Zhang, Fu‐Min

doi:10.1016/j.rsci.2020.11.007

Cited by 2 publications

(1 citation statement)

References 42 publications

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“…Furthermore, the origin and geographic distribution of DPL were investigated using 132 O. sativa , 296 accessions of O. nivara , and 388 accessions of O. rufipogon. DPL1 − and DPL2 − haplotypes of O. sativa separately emerged from an O. nivara population in India and O. rufipogon in South China, subsequently spread into other groups, especially aus and temperate japonica , respectively (Mizuta et al, 2010 ; Xu et al, 2021 ). Therefore, hybrid incompatibility established by DPL contributed to the genetic differentiation between aus and temperate japonica subspecies.…”

Section: The Origin the Evolution Of Hybrid Sterility Loci And The Di...mentioning

confidence: 99%

Understanding the Nature of Hybrid Sterility and Divergence of Asian Cultivated Rice

Wang¹,

Pu²,

Yang³

et al. 2022

Front. Plant Sci.

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Intraspecific hybrid sterility is a common form of postzygotic reproductive isolation in Asian cultivated rice, which is also the major obstacle to utilize the strong heterosis in the rice breeding program. Here, we review recent progress in classification and hybrid sterility in Asian cultivated rice. A genome-wide analysis of numerous wild relatives of rice and Asian cultivated rice has provided insights into the origin and differentiation of Asian cultivated rice, and divided Asian cultivated rice into five subgroups. More than 40 conserved and specific loci were identified to be responsible for the hybrid sterility between subgroup crosses by genetic mapping, which also contributed to the divergence of Asian cultivated rice. Most of the studies are focused on the sterile barriers between indica and japonica crosses, ignoring hybrid sterility among other subgroups, leading to neither a systematical understanding of the nature of hybrid sterility and subgroup divergence, nor effectively utilizing strong heterosis between the subgroups in Asian cultivated rice. Future studies will aim at identifying and characterizing genes for hybrid sterility and segregation distortion, comparing and understanding the molecular mechanism of hybrid sterility, and drawing a blueprint for intraspecific hybrid sterility loci derived from cross combinations among the five subgroups. These studies would provide scientific and accurate guidelines to overcome the intraspecific hybrid sterility according to the parent subgroup type identification, allowing the utilization of heterosis among subgroups, also helping us unlock the mysterious relationship between hybrid sterility and Asian cultivated rice divergence.

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Section: The Origin the Evolution Of Hybrid Sterility Loci And The Di...mentioning

confidence: 99%

Understanding the Nature of Hybrid Sterility and Divergence of Asian Cultivated Rice

Wang¹,

Pu²,

Yang³

et al. 2022

Front. Plant Sci.

View full text Add to dashboard Cite

show abstract

AlignStatPlot: An R package and online tool for robust sequence alignment statistics and innovative visualization of big data

Alsamman,

El Allali,

Mokhtar

et al. 2023

PLoS ONE

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Multiple sequence alignment (MSA) is essential for understanding genetic variations controlling phenotypic traits in all living organisms. The post-analysis of MSA results is a difficult step for researchers who do not have programming skills. Especially those working with large scale data and looking for potential variations or variable sample groups. Generating bi-allelic data and the comparison of wild and alternative gene forms are important steps in population genetics. Customising MSA visualisation for a single page view is difficult, making viewing potential indels and variations challenging. There are currently no bioinformatics tools that permit post-MSA analysis, in which data on gene and single nucleotide scales could be combined with gene annotations and used for cluster analysis. We introduce “AlignStatPlot,” a new R package and online tool that is well-documented and easy-to use for MSA and post-MSA analysis. This tool performs both traditional and cutting-edge analyses on sequencing data and generates new visualisation methods for MSA results. When compared to currently available tools, AlignStatPlot provides a robust ability to handle and visualise diversity data, while the online version will save time and encourage researchers to focus on explaining their findings. It is a simple tool that can be used in conjunction with population genetics software.

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Genetic and Geographic Patterns of Duplicate DPL Genes Causing Genetic Incompatibility Within Rice: Implications for Multiple Domestication Events in Rice

Cited by 2 publications

References 42 publications

Understanding the Nature of Hybrid Sterility and Divergence of Asian Cultivated Rice

Understanding the Nature of Hybrid Sterility and Divergence of Asian Cultivated Rice

AlignStatPlot: An R package and online tool for robust sequence alignment statistics and innovative visualization of big data

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