Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2021 Jun;19(2):e19.
doi: 10.5808/gi.21024. Epub 2021 Jun 30.

Analysis of genome variants in dwarf soybean lines obtained in F6 derived from cross of normal parents (cultivated and wild soybean)

Neha Samir Roy  1 , Yong-Wook Ban  2 , Hana Yoo  1 , Rahul Vasudeo Ramekar  1 , Eun Ju Cheong  2 , Nam-Il Park  3 , Jong Kuk Na  4 , Kyong-Cheul Park  1 , Ik-Young Choi  1
Affiliations

Analysis of genome variants in dwarf soybean lines obtained in F6 derived from cross of normal parents (cultivated and wild soybean)

Neha Samir Roy et al. Genomics Inform. 2021 Jun.

Abstract

Plant height is an important component of plant architecture and significantly affects crop breeding practices and yield. We studied DNA variations derived from F5 recombinant inbred lines (RILs) with 96.8% homozygous genotypes. Here, we report DNA variations between the normal and dwarf members of four lines harvested from a single seed parent in an F6 RIL population derived from a cross between Glycine max var. Peking and Glycine soja IT182936. Whole genome sequencing was carried out, and the DNA variations in the whole genome were compared between the normal and dwarf samples. We found a large number of DNA variations in both the dwarf and semi-dwarf lines, with one single nucleotide polymorphism (SNP) per at least 3.68 kb in the dwarf lines and 1 SNP per 11.13 kb of the whole genome. This value is 2.18 times higher than the expected DNA variation in the F6 population. A total of 186 SNPs and 241 SNPs were discovered in the coding regions of the dwarf lines 1282 and 1303, respectively, and we discovered 33 homogeneous nonsynonymous SNPs that occurred at the same loci in each set of dwarf and normal soybean. Of them, five SNPs were in the same positions between lines 1282 and 1303. Our results provide important information for improving our understanding of the genetics of soybean plant height and crop breeding. These polymorphisms could be useful genetic resources for plant breeders, geneticists, and biologists for future molecular biology and breeding projects.

Keywords: RIL population; SNP; dwarf; soybean; whole genome sequencing; wild type.

PubMed Disclaimer

Conflict of interest statement

Conflicts of Interest

No potential conflict of interest relevant to this article was reported.

Figures

Fig. 1.
Fig. 1.
Schematic representation of dwarf recombinant inbred lines (RIL) development. Glycine max var. Peking and G. soja var. IT182936 were crossed to develop RIL lines. From F2 few lines exhibited dwarf phenotype and continued to appear dwarf in their successive generation. Two such lines from the F6 generation were chosen for analysis.
Fig. 2.
Fig. 2.
Single nucleotide polymorphism (SNP) per kb of gene length in dwarf soybean lines. The frequency of SNP in dwarf lines was observed significantly higher than expected. Dwarf lines exhibited SNP on every 3.68 kb of genome whereas the expected length of the genome should be 23.99 kb. RIL, recombinant inbred lines.
Fig. 3.
Fig. 3.
Distribution of missense single nucleotide polymorphisms (SNPs) in the soybean genome in genic regions. NB-ARC, nucleotide-binding APAF-1 R proteins and CED-4; TIR-NBS-LRR, toll interleukin 1 receptor nucleotide-binding site leucine-rich repeat resistance proteins.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

References

    1. Fried HG, Narayanan S, Fallen B. Evaluation of soybean [Glycine max (L.) Merr.] genotypes for yield, water use efficiency, and root traits. PLoS One. 2019;14:e0212700. - PMC - PubMed
    1. Shin DH. Utilization of soybean as food stuffs in Korea. In: El-Shemy H, editor. Soybean and Nutrition. London: IntechOpen; 2011. pp. 81–110.
    1. Zhang Y, Yu C, Lin J, Liu J, Liu B, Wang J, et al. OsMPH1 regulates plant height and improves grain yield in rice. PLoS One. 2017;12:e0180825. - PMC - PubMed
    1. Milach SC, Federizzi LC. Dwarfing genes in plant improvement. Adv Agron. 2001;73:35–63.
    1. Kuraparthy V, Sood S, Gill BS. Genomic targeting and mapping of tiller inhibition gene (tin3) of wheat using ESTs and synteny with rice. Funct Integr Genomics. 2008;8:33–42. - PubMed

LinkOut - more resources