Development of SNP Markers from GWAS for Selecting Seed Coat and Aleurone Layers in Brown Rice ( L.)

Overview

Journal Genes (Basel)

Publisher MDPI

Date 2022 Oct 27

PMID 36292692

Authors

Me-Sun Kim

Seo-Rin Ko

Van Trang Le

Moo-Gun Jee

Yu Jin Jung

Kwon-Kyoo Kang

Yong-Gu Cho

Affiliations

Soon will be listed here.

Abstract

Ninety-five percent of the general nutrients in rice are concentrated in the rice bran and germ, and many nutrients such as vitamins, minerals, dietary fiber, and essential fatty acids, as well as antioxidants such as tocopherol, are lost during milling. In this study, we investigated the thickness of seed coat and aleurone layers using a 294 rice core collection, and found candidate genes related to thickness of seed coat and aleurone layers, by performing a genome wide association study (GWAS) analysis using whole genome resequencing data. Two primer pairs that can be used as high-resolution melting (HRM) markers were developed. As a result of genotyping BCF individuals derived from a cross between "Samgwang" and "Seolgaeng", and using corresponding HRM markers, it was possible to finally develop HRM markers for selecting seed coat and aleurone layer thickness. This is expected to be used as basic data for the application of gene editing using CRISPR/Cas9 technology and for establishing a breeding strategy for high eating quality rice using molecular genetic technology.

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References

Rozen S, Skaletsky H . Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol. 1999; 132:365-86. DOI: 10.1385/1-59259-192-2:365. View

Gabriel S, Schaffner S, Nguyen H, Moore J, Roy J, Blumenstiel B . The structure of haplotype blocks in the human genome. Science. 2002; 296(5576):2225-9. DOI: 10.1126/science.1069424. View

Huang X, Wei X, Sang T, Zhao Q, Feng Q, Zhao Y . Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet. 2010; 42(11):961-7. DOI: 10.1038/ng.695. View

. The 3,000 rice genomes project. Gigascience. 2014; 3:7. PMC: 4035669. DOI: 10.1186/2047-217X-3-7. View

Irshad F, Li C, Wu H, Yan Y, Xu J . The Function of DNA Demethylase Gene ROS1a Null Mutant on Seed Development in Rice () Using the CRISPR/CAS9 System. Int J Mol Sci. 2022; 23(12). PMC: 9223687. DOI: 10.3390/ijms23126357. View

Schatz M, Maron L, Stein J, Wences A, Gurtowski J, Biggers E . Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica. Genome Biol. 2014; 15(11):506. PMC: 4268812. DOI: 10.1186/PREACCEPT-2784872521277375. View

Barrett J, Fry B, Maller J, Daly M . Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics. 2004; 21(2):263-5. DOI: 10.1093/bioinformatics/bth457. View

Korte A, Farlow A . The advantages and limitations of trait analysis with GWAS: a review. Plant Methods. 2013; 9:29. PMC: 3750305. DOI: 10.1186/1746-4811-9-29. View

Huang X, Han B . Natural variations and genome-wide association studies in crop plants. Annu Rev Plant Biol. 2013; 65:531-51. DOI: 10.1146/annurev-arplant-050213-035715. View

10.

Rueden C, Schindelin J, Hiner M, DeZonia B, Walter A, Arena E . ImageJ2: ImageJ for the next generation of scientific image data. BMC Bioinformatics. 2017; 18(1):529. PMC: 5708080. DOI: 10.1186/s12859-017-1934-z. View

11.

Zhao K, Tung C, Eizenga G, Wright M, Ali M, Price A . Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nat Commun. 2011; 2:467. PMC: 3195253. DOI: 10.1038/ncomms1467. View

12.

Li H, Durbin R . Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009; 25(14):1754-60. PMC: 2705234. DOI: 10.1093/bioinformatics/btp324. View

13.

Huggins T, Chen M, Fjellstrom R, Jackson A, McClung A, Edwards J . Association Analysis of Three Diverse Rice ( L.) Germplasm Collections for Loci Regulating Grain Quality Traits. Plant Genome. 2019; 12(1). DOI: 10.3835/plantgenome2017.09.0085. View

14.

Han Z, Zhang J, Cai S, Chen X, Quan X, Zhang G . Association mapping for total polyphenol content, total flavonoid content and antioxidant activity in barley. BMC Genomics. 2018; 19(1):81. PMC: 5784657. DOI: 10.1186/s12864-018-4483-6. View

15.

Shobana S, Malleshi N, Sudha V, Spiegelman D, Hong B, Hu F . Nutritional and sensory profile of two Indian rice varieties with different degrees of polishing. Int J Food Sci Nutr. 2011; 62(8):800-10. PMC: 6512801. DOI: 10.3109/09637486.2011.585962. View

16.

Liu C, Chen K, Zhao X, Wang X, Shen C, Zhu Y . Identification of genes for salt tolerance and yield-related traits in rice plants grown hydroponically and under saline field conditions by genome-wide association study. Rice (N Y). 2019; 12(1):88. PMC: 6889114. DOI: 10.1186/s12284-019-0349-z. View

17.

Sakai H, Kanamori H, Arai-Kichise Y, Shibata-Hatta M, Ebana K, Oono Y . Construction of pseudomolecule sequences of the aus rice cultivar Kasalath for comparative genomics of Asian cultivated rice. DNA Res. 2014; 21(4):397-405. PMC: 4131834. DOI: 10.1093/dnares/dsu006. View

18.

Wang X, Kim K, Chu S, Phitaktansakul R, Park S, Chung I . Genome-Wide Association Study for Squalene Contents and Functional Haplotype Analysis in Rice. ACS Omega. 2019; 4(21):19358-19365. PMC: 6868895. DOI: 10.1021/acsomega.9b02754. View

19.

Brachi B, Morris G, Borevitz J . Genome-wide association studies in plants: the missing heritability is in the field. Genome Biol. 2011; 12(10):232. PMC: 3333769. DOI: 10.1186/gb-2011-12-10-232. View

20.

Wang X, Jia M, Ghai P, Lee F, Jia Y . Genome-Wide Association of Rice Blast Disease Resistance and Yield-Related Components of Rice. Mol Plant Microbe Interact. 2015; 28(12):1383-92. DOI: 10.1094/MPMI-06-15-0131-R. View