The patterns of deleterious mutations during the domestication of soybean

Kim, Myung-Shin; Lozano, Roberto; Kim, Ji Eun; Bae, Dong Nyuk; Kim, Sang‐Tae; Park, Jung Ho; Choi, Man Soo; Kim, Jae Hyun; Ok, Hyun-Choong; Park, Soo-Kwon; Gore, Michael A.; Moon, Jung‐Kyung; Jeong, Soon-Chun

doi:10.1038/s41467-020-20337-3

Cited by 81 publications

(90 citation statements)

References 107 publications

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“…Direct comparison between corresponding chromosome sequences of the Hwangkeum and Williams 82 assemblies identified 1,788,320 SNPs and 517,907 indels (< 50 bp) (Table S6 and File S2). Interestingly, the number of SNPs is similar to the combined number (1,678,164) of heterozygous (4,919), missing (713,953), and homozygous non-reference (959,292) SNPs for Hwangkeum in the 30,753,511 SNP set without the minor allele frequency filter detected in the 781 soybean haplotype map set (Kim et al 2021). The number of indels is also similar to the combined number (470,389) of heterozygous (28,639), missing (303,784), and homozygous non-reference (137,966) indels for Hwangkeum in the 5,717,052 indel set without the minor allele frequency filtration detected from the same set.…”

Section: Genome Structure Comparison With Other Publicly Available Soybean Genomesmentioning

confidence: 69%

“…After three weeks' growth, a bulk of young trifoliolate leaf tissues was collected for genomic DNA extraction. Note that the seeds of Hwangkeum used in this study came from the line of Hwangkeum that had been subject to single plant selection at least twice during our recent 180K SoyaSNP array and genome resequencing studies (Lee et al 2015;Kim et al 2021). Genomic DNAs for the generation of Illumina short-read (Illumina, San Diego, CA, USA) and PacBio SMRT long-read sequences (Pacific Biosciences, Menlo Park, CA, USA) were extracted using the CTAB method, as described by Saghai-Maroof et al (1984).…”

Section: Plant Materials and Sequencingmentioning

confidence: 99%

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Genome Assembly of the Popular Korean Soybean Cultivar Hwangkeum

Kim

Lee

Baek

et al. 2021

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Massive resequencing efforts have been undertaken to catalog allelic variants in major crop species including soybean, but the scope of the information for genetic variation often depends on short sequence reads mapped to the extant reference genome. Additional de novo assembled genome sequences provide a unique opportunity to explore a dispensable genome fraction in the pan-genome of a species. Here, we report the de novo assembly and annotation of Hwangkeum, a popular soybean cultivar in Korea. The assembly was constructed using PromethION nanopore sequencing data and two genetic maps, and was then error-corrected using Illumina short-reads and PacBio SMRT reads. The 933.12 Mb assembly was annotated 79,870 transcripts for 58,550 genes using RNA-Seq data and the public soybean annotation set. Comparison of the Hwangkeum assembly with the Williams 82 soybean reference genome sequence revealed 1.8 million single-nucleotide polymorphisms, 0.5 million indels, and 25 thousand putative structural variants. However, there was no natural megabase-scale chromosomal rearrangement. Incidentally, by adding two novel groups, we found that soybean contains four clearly separated groups of centromeric satellite repeats. Analyses of satellite repeats and gene content suggested that the Hwangkeum assembly is a high-quality assembly. This was further supported by comparison of the marker arrangement of anthocyanin biosynthesis genes and of gene arrangement at the Rsv3 locus. Therefore, the results indicate that the de novo assembly of Hwangkeum is a valuable additional reference genome resource for characterizing traits for the improvement of this important crop species.

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Section: Genome Structure Comparison With Other Publicly Available Soybean Genomesmentioning

confidence: 69%

Section: Plant Materials and Sequencingmentioning

confidence: 99%

Genome Assembly of the Popular Korean Soybean Cultivar Hwangkeum

Kim

Lee

Baek

et al. 2021

Preprint

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“…Our estimate of nucleotide diversity loss was higher than previous estimates for domesticated sorghum based on nuclear microsatellite markers (e.g., 14%, Casa et al, 2005 ), but lower than the loss recorded in other main crops with selfing or mixed mating systems. For instance, it was estimated a 62% nucleotide diversity reduction in rice (Caicedo et al, 2007 ), 72% in common beans (Bitocchi et al, 2013 ) and 50% in soybean (Kim et al, 2021 ). Domesticated sorghum also showed lower expression variation than the wild accessions, a finding common to other crops such as maize (Lemmon et al, 2014 ) and common bean (Bellucci et al, 2014 ) but also animal domesticates (Liu et al, 2019 ).…”

Section: Discussionmentioning

confidence: 99%

The Road to Sorghum Domestication: Evidence From Nucleotide Diversity and Gene Expression Patterns

et al. 2021

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Native African cereals (sorghum, millets) ensure food security to millions of low-income people from low fertility and drought-prone regions of Africa and Asia. In spite of their agronomic importance, the genetic bases of their phenotype and adaptations are still not well-understood. Here we focus on Sorghum bicolor, which is the fifth cereal worldwide for grain production and constitutes the staple food for around 500 million people. We leverage transcriptomic resources to address the adaptive consequences of the domestication process. Gene expression and nucleotide variability were analyzed in 11 domesticated and nine wild accessions. We documented a downregulation of expression and a reduction of diversity both in nucleotide polymorphism (30%) and gene expression levels (18%) in domesticated sorghum. These findings at the genome-wide level support the occurrence of a global reduction of diversity during the domestication process, although several genes also showed patterns consistent with the action of selection. Nine hundred and forty-nine genes were significantly differentially expressed between wild and domesticated gene pools. Their functional annotation points to metabolic pathways most likely contributing to the sorghum domestication syndrome, such as photosynthesis and auxin metabolism. Coexpression network analyzes revealed 21 clusters of genes sharing similar expression patterns. Four clusters (totaling 2,449 genes) were significantly enriched in differentially expressed genes between the wild and domesticated pools and two were also enriched in domestication and improvement genes previously identified in sorghum. These findings reinforce the evidence that the combined and intricated effects of the domestication and improvement processes do not only affect the behaviors of a few genes but led to a large rewiring of the transcriptome. Overall, these analyzes pave the way toward the identification of key domestication genes valuable for genetic resources characterization and breeding purposes.

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“…Maldonado et al 23 sequenced 28 soybean cultivars of Brazilian, analyzed in detail the possible effects of SNPs and InDels with non-synonymous mutations on the function of the corresponding genes, and suggested that once the effect of these mutations on gene function were con rmed, then the adaptation mechanism of soybean to tropical conditions in Brazil could be explained. Kim et al 24 carried out high-depth (> 13x) whole-genome (WGS) analysis of 418 domesticated soybean cultivars, 345 wild soybean materials and 18 natural hybrid varieties. The whole genome variation map of soybean was obtained, and 10.6 million SNPs and 1.4 million InDels were identi ed.…”

Section: Introductionmentioning

confidence: 99%

Putative Variants, Genetic Diversity and Population Structure among Soybean Cultivars Bred at Different Ages in Huang-Huai-Hai Region

Liu

Xie

Lin

et al. 2021

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Soybean cultivars bred in the Huang-Huai-Hai region (HR) are rich in pedigree information. To data, few reports have exposed the genetic variants, population structure and genetic diversity of cultivars in this region by making use of genome-wide resequencing data. To depict genetic variation, population structure and composition characteristics of genetic diversity, a sample of soybean population that composed all by cultivars was constructed. We re-sequenced 181 soybean cultivar genomes with an average depth of 10.38x. In total, 11185589 single nucleotide polymorphisms (SNPs) and 2520208 insertion-deletions (InDels) were identified on all 20 chromosomes. A considerable number of putative variants existed in important genome regions that may have an incalculable influence on genes, which participated in momentous biological processes. PCA and population structure figured out that there was no obvious grouping trend. The LD semi-decay distances of the five sub-populations were 290kb, 380kb, 753kb, 182kb, and 227kb, respectively. Sub-population A (SA) had the highest value of nucleotide polymorphism (π). With the passage of time, the nucleotide polymorphism of SB and SC decreased gradually, however that of SD and SE, opposite to SB and SC, gave a rapid up-climbing trend, which meant a sharp increasing in genetic diversity during the latest 20 years, hinting that breeders may have different breeding goals in different breeding periods in HR. Analysis of the PIC statistics exhibited very similar results with π. The current study was to analyze the genetic variants and characterize the structure and genetic diversity of soybean cultivars bred in different decades in HR, and in the hope of providing a theoretical reference for other identical studies.

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The patterns of deleterious mutations during the domestication of soybean

Cited by 81 publications

References 107 publications

Genome Assembly of the Popular Korean Soybean Cultivar Hwangkeum

Genome Assembly of the Popular Korean Soybean Cultivar Hwangkeum

The Road to Sorghum Domestication: Evidence From Nucleotide Diversity and Gene Expression Patterns

Putative Variants, Genetic Diversity and Population Structure among Soybean Cultivars Bred at Different Ages in Huang-Huai-Hai Region

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