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    Home > Food News > Food Articles > The effect of inter-species hybridization on the reduction of genetic bottlenecks in soybean domestication | Genome Biology

    The effect of inter-species hybridization on the reduction of genetic bottlenecks in soybean domestication | Genome Biology

    • Last Update: 2021-03-14
    • Source: Internet
    • Author: User
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    Journal:
    Xutong Wang, Liyang Chen and Jianxin Ma
    Published: 2019/01/30
    Digital ID: 10.1186/s13059-019 -1631-5
    Original Link:
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    Soybean (Glycine max (L.) Merr. is an important both grain and oil crop and an important source of plant protein in human life. Soybean cultivation is widely believed to have originated in China and was domesticated by Glycine soja about 6,000 to 9,000 years ago. This idea of a single origin is also supported by recently identified domesticated genes. Still, the history and process of soybean domestication is still controversial. According to the sequencing results of soybean genome, the differentiation between wild soybeans and cultivated varieties has reached a time frame of about 270,000 years, so the development of wild soybeans to soybean cultivation is considered a gradual process. In China's soybean-growing areas, there are still semi-wild soybeans in the form of wild soybeans and domesticated soybeans (Glycine gracilis).
    speculates that there may be a gene flow from wild soybeans to cultivated soybeans.
    gene flow between gene pools, produced by intersequenc hybridization, is an important cause of gene flow. Gene infiltration has been reported in crops such as corn and rice, but there has been no in-depth study of the evolutionary patterns of gene infiltration during crop domestication and the results. Recently, a team of professors at Purdue University in the United States used resequencing data on soybean species published by others to reveal the genome fragments and gene infiltration patterns, causes and dynamic evolutionary results of the nucleus and chloroengues between wild soybeans and cultivated soybeans by comparing and evolving genomes.
    the study, by analyzing the homogeneity of 302 soybean species (Identical By Descent, IBD), found interseth gene penetration fragments in almost all soybean materials. Sixty-two wild soybean materials and 129 farm species in this group did not experience artificially mediated sexual hybridization, so the proportion of infiltration fragments detected in each material (Figure 1) and the distribution of these fragments in each chromosome (Figure 2) should be the result of natural and artificial selection during soybean domestication. The study found that the proportion of penetration fragments in the near grain region in wild soybeans and cultivated soybeans was higher than that in the chromosomal arm, which may be related to the low recombination rate and the partial accumulation of harmful mutations in the area near the silk particle point. The results of the D-statics test show that these infiltration fragments are derived from gene flow (Figure 3) rather than from the incomplete lineage sorting effect.

    the study further analyzed the geographical distribution of representative materials with large-fragment genome penetration and the genetic diversity of the whole genome and local areas of the genome (Figure 4). Among them, there are 33% and 31% penetration fragments in wild soybean material PI 578357 (s61) and local varieties PI 393734 (m30), respectively. s61 comes from the Russian state of Amur on the other side of the Heilongjiang River, and the infiltration section on chromosome 2 is very similar to the evolutionary tree of the farm species "Black River Soybean" (m104) from the Heihe region of Heilongjiang Province, while the non-infiltration section of s61 is very similar to another wild soybean material s5 from Russia's coastal region, and the material has a great difference in the whole genome evolutionary relationship. Given the proximity of the three regions, chromosomal chimerism detected in s61 may have originated from interbreeding between m30 and s5 (or materials close to their relatives). Similarly, a similar phenomenon was found in chromosome 19 of the local species m30, which was collected on the Korean peninsula, most likely as a result of the hybridization of local species m111 and wild soybean s42 on the Korean peninsula. Based on genome-wide sequences, it is inferred that s61 and m104 and m30 and s42 were differentiated about 370,000 and 270,000 years ago, and that the pattern of genomic fragments between them should be direct evidence of hybridization between cultivated and wild species during soybean domestication.Theoretically, the offspring materials produced by hybridization and re-interbreeding between wild and cultivated species undergo natural and artificial selection: the former chooses the adaptive nature of the natural environment, while the latter chooses the domesticated nature that is good for agricultural production and human consumption. The study showed that the proportion of cultivated soybeans permeated in the selective removal of artificial domestication in wild varieties was lower than that of other segments, while the proportion of wild soybeans permeated in this segment was lower than that of other segments in cultivated varieties. The proportion of the above-mentioned penetration fragments is lower in the QTL interval of the control domestication symptoms (Figure 5). These observations showed the different selection effects of natural and artificial selection after hybridization and return of cultivated soybeans and wild soybeans. The study also looked at domesticated genes (GmHs1-1; B1) Selective removal of the location of the ? The SNP information in the selective sweep section was analysed and genetic infiltration was found in both regions (Figure 6).

    study also explores the evolutionary relationship between wild and cultivated soybean middle-leaf green genomes. The evolutionary differentiation of cultivated soybean chlorophytes is significantly smaller than that of wild soybeans, but some cultivated soybeans contain the chlorophyte genome of wild soybean type, and some wild soybeans detect the chlorophyte genome of cultivated soybean type (Figure 7). This observation provides new evidence of natural hybridization between wild soybeans and cultivated soybeans. The nuclear genome and the stethosome genome generally show a co-evolutionary trend, but some materials have non-parallel evolution between the nucleus and the stethosome genome, which may be the result of natural hybridization within the species.with the massive loss of genetic diversity, is the main genetic bottleneck in crop formation. However, compared with wild soybeans, there is still a high genetic diversity in cultivated soybeans. It is estimated that the average differentiation time between cultivated soybean individuals dates back 300,000 years (Figure 8), and such high diversity is often not available through artificial selection of a small number of wild materials in a particular area. This study reveals the effect of interseth hybridization on genetic bottleneck in soybean domestication process, and has guiding significance for the in-depth understanding of crop domestication process and the evaluation and utilization of species resources.
    the above research results have been published online
    online, the title is "Genomic introgresion through interspecific hybridization of the act of genetic basic when domestication." Professor
    , Department of Agomy and Center for Plant Biology, Purdue University, USA, is the author of the newsletter, Dr.
    is the first author and Ph.D. graduate student Yang Chen is the co-author.
    Evidence of introgression, the transfer of genetic material, between crops and their wild relatives through spontaneous hybridization and subsequent backcrossing has been documented; however, the evolutionary patterns and consequences of introgression and its influence on the processes of crop domestication and varietal diversification are poorly understood.We investigate the genomic landscape and evolution of putative crop-wild-relative introgression by analyzing the nuclear and chloroplast genomes from a panel of wild (Glycine soja) and domesticated (Glycine max) soybeans. Our data suggest that naturally occurring introgression between wild and domesticated soybeans was widespread and that introgressed variation in both wild and domesticated soybeans was selected against throughout the genomes and preferentially removed from the genomic regions underlying selective sweeps and domestication quantitative trait locus (QTL). In both taxa, putative introgression was preferentially retained in recombination-repressed pericentromeric regions that exhibit lower gene densities, reflecting potential roles of recombination in purging introgression. Despite extensive removal of introgressed variation by recurrent selection for domestication-related QTL and associated genomic regions, spontaneous interspecific hybridization during soybean domestication appear to have contributed to a rapid varietal diversification with high levels of genetic diversity and asymmetric evolution between the nuclear and chloroplast genomes.This work reveals the evolutionary forces, patterns, and consequences of putative genomic introgression between crops and their wild relatives, and the effects of introgression on the processes of crop domestication and varietal diversification. We envision that interspecific introgression serves as an important mechanism for counteracting the reduction of genetic diversity in domesticated crops, particularly the ones under single domestication.(
    ) publishes outstanding research in all areas of biology and biomedicine studied from a genomic and post-genomic perspective.
    (Source: Science.com)
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