Identification and molecular mapping of the semi-dwarf locus (sdf-1) in soybean by SLAF-seq method

Dong, Zhimin; Chen, Liang; Li, Zhi; Liu, Nianxi; Zhang, Shichen; Liu, Jia; Liu, Baoquan

doi:10.1007/s10681-020-02633-7

Cited by 6 publications

(3 citation statements)

References 46 publications

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“…Compared to re-sequence's needing to smash genomes without distinction through ultrasounds and sequence and splice the broken fragments, SLAF-seq only needs to undergo systematic evaluation, select restriction endonucleases that can evenly cleave genomes, sequence the cleaved fragments one by one, and splice them according to the cleaved sites. SLAF-seq optimizes labeling efficiency on the basis of re-sequence and ensures the labeling density while reducing the difficulty and costs of sequencing [ 16 , 17 ]. In summary, GWAS based on SLAF-seq is more suitable for the research targeting medium populations.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide association study and high-quality gene mining related to soybean protein and fat

Zhang,

Sun,

Wang

et al. 2023

BMC Genomics

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Background Soybean is one of the most important oil crops in the world, and its protein and fat are the primary sources of edible oil and vegetable protein. The effective components in soybean protein and fat have positive effects on improving human immunity, anti-tumor, and regulating blood lipids and metabolism. Therefore, increasing the contents of protein and fat in soybeans is essential for improving the quality of soybeans. Results This study selected 292 soybean lines from different regions as experimental materials, based on SLAF-seq sequencing technology, and performed genome-wide association study (GWAS) on the phenotype data from 2019–2021 Planted at the experimental base of Jilin Agricultural University, such as the contents of protein and fat of soybeans. Through the GLM model and MLM model, four SNP sites (Gm09_39012959, Gm12_35492373, Gm16_9297124, and Gm20_24678362) that were significantly related to soybean fat content were associated for three consecutive years, and two SNP sites (Gm09_39012959 and Gm20_24678362) that were significantly related to soybean protein content were associated. By the annotation and enrichment of genes within the 100 Kb region of SNP loci flanking, two genes (Glyma.09G158100 and Glyma.09G158200) related to soybean protein synthesis and one gene (Glyma.12G180200) related to lipid metabolism were selected. By the preliminary verification of expression levels of genes with qPCR, it is found that during the periods of R6 and R7 of the accumulation of soybean protein and fat, Glyma.09G158100 and Glyma.09G158200 are positive regulatory genes that promote protein synthesis and accumulation, while Glyma.12G180200 is the negative regulatory gene that inhibits fat accumulation. Conclusions These results lay the basis for further verifying the gene function and studying the molecular mechanisms regulating the accumulation of protein and fat in soybean seeds.

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Section: Introductionmentioning

confidence: 99%

Genome-wide association study and high-quality gene mining related to soybean protein and fat

Zhang,

Sun,

Wang

et al. 2023

BMC Genomics

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“…A dwarf mutant from fast neutron bombardment has an 803 bp deletion in the first exon of Glyma15g05831 ( Hwang et al., 2015 ). The sdf-1 locus was mapped to an 80.72 kb region on Chr 19 of soybean ( Dong et al., 2020 ). GmIAA27 relies on auxin to interact with TIR1, and control a dmbn mutant plants ( Su et al., 2022 ).…”

Section: Introductionmentioning

confidence: 99%

Genetic dissection of the soybean dwarf mutant dm with integrated genomic, transcriptomic and methylomic analyses

Jiang

Wang²,

Huang³

et al. 2022

Front. Plant Sci.

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Plant height affects crop production and breeding practices, while genetic control of dwarfism draws a broad interest of researchers. Dwarfism in soybean (Glycine max) is mainly unexplored. Here, we characterized a dwarf mutant dm screened from ethyl methanesulfonate (EMS) mutated seeds of the soybean cultivar Zhongpin 661(ZP). Phenotypically, dm showed shorter and thinner stems, smaller leaves, and more nodes than ZP under greenhouse conditions. Genetically, whole-genome sequencing and comparison revealed that 210K variants of SNPs and InDel in ZP relative to the soybean reference genome Williams82, and EMS mutagenesis affected 636 genes with variants predicted to have a large impact on protein function in dm. Whole-genome methylation sequencing found 704 differentially methylated regions in dm. Further whole-genome RNA-Seq based transcriptomic comparison between ZP and dm leaves revealed 687 differentially expressed genes (DEGs), including 263 up-regulated and 424 down-regulated genes. Integrated omics analyses revealed 11 genes with both differential expressions and DNA variants, one gene with differential expression and differential methylation, and three genes with differential methylation and sequence variation, worthy of future investigation. Genes in cellulose, fatty acids, and energy-associated processes could be the key candidate genes for the dwarf phenotype. This study provides genetic clues for further understanding of the genetic control of dwarfism in soybean. The genetic resources could help to inbreed new cultivars with a desirable dwarf characteristic.

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“…For example, Sun et al used 50,530 SLAFs with 13,291 SNPs to genotype the F1 population of the common carp [24]. Due to its e cient identi cation of SNP markers, SLAF-seq has been used in a wide variety of crops [26][27][28][29][30]. SLAF-seq was also used to develop the rst high-density genetic maps for several economically important species, including sesame [31], cucumber [23], the brown alga Undaria pinnati da (Phaeophyceae) [32], wax gourd [33], watermelon (Citrullus lanatus L.) [34], and Salvia miltiorrhiza [25].…”

Section: Introductionmentioning

confidence: 99%

Investigation of Genetic Relationships within Miscanthus Using Snp Markers Identified Using Slaf-Seq

Chen¹,

Huang²,

Yi³

et al. 2020

SSRN Journal

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Background: Miscanthus, which is a leading dedicated-energy grass in Europe and in parts of Asia, is expected to play a key role in the development of the future bioeconomy. However, due to its complex genetic background, it is di cult to investigate phylogenetic relationships and the evolution of gene function in this genus. Here, we investigated 50 Miscanthus germplasms: 1 female parent (M. lutarioriparius), 30 candidate male parents (M. lutarioriparius, M. sinensis, and M. sacchari orus), and 19 offspring. We used high-throughput Speci c-Locus Ampli ed Fragment sequencing (SLAF-seq) to identify informative single nucleotide polymorphisms (SNPs) in all germplasms.Results: We identi ed 800,081 SLAF tags, of which 160,368 were polymorphic. Each tag was 264-364 bp long. The obtained SNPs were used to investigate genetic relationships within Miscanthus. We constructed a phylogenetic tree of the 50 germplasms using the obtained SNPs, and found that the germplasms fell into two clades: one clade of M. sinensis only and one clade that included the offspring, M. lutarioriparius, and M. sacchari orus. Genetic cluster analysis indicated that M. lutarioriparius germplasm C3 was the most likely male parent of the offspring.Conclusions: As a high-throughput sequencing method, SLAF-seq can be used to identify informative SNPs in Miscanthus germplasms and to rapidly characterize genetic relationships within this genus. Our results will support the development of breeding programs utilizing Miscanthus cultivars with elite biomass-or ber-production potential.

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Identification and molecular mapping of the semi-dwarf locus (sdf-1) in soybean by SLAF-seq method

Cited by 6 publications

References 46 publications

Genome-wide association study and high-quality gene mining related to soybean protein and fat

Genome-wide association study and high-quality gene mining related to soybean protein and fat

Genetic dissection of the soybean dwarf mutant dm with integrated genomic, transcriptomic and methylomic analyses

Investigation of Genetic Relationships within Miscanthus Using Snp Markers Identified Using Slaf-Seq

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