Genome-wide Association Study and Candidate Gene Identification for Agronomic Traits in 182 Upward-growing Fruits of C. Frutescens and C. Annuum

Overview

Journal Sci Rep

Specialty Science

Date 2024 Jun 26

PMID 38926509

Authors

Genying Fu

Shuang Yu

Kun Wu

Mengxian Yang

Muhammad Ahsan Altaf

Zhuo Wu

Qin Deng

Xu Lu

Huizhen Fu

Zhiwei Wang

Shanhan Cheng

Affiliations

Soon will be listed here.

Abstract

Pepper agronomic traits serve as pivotal indicators for characterizing germplasm attributes and correlations. It is important to study differential genotypic variation through phenotypic differences of target traits. Whole genome resequencing was used to sequence the whole genome among different individuals of species with known reference genomes and annotations, and based on this, differential analyses of individuals or populations were carried out to identify SNPs for agronomic traits related to pepper. This study conducted a genome-wide association study encompassing 26 key agronomic traits in 182 upward-growing fruits of C. frutescens and C. annuum. The population structure (phylogenetics, population structure, population principal component analysis, genetic relationship) and linkage disequilibrium analysis were realized to ensure the accuracy and reliability of GWAS results, and the optimal statistical model was determined. A total of 929 SNPs significantly associated with 26 agronomic traits, were identified, alongside the detection of 519 candidate genes within 100 kb region adjacent to these SNPs. Additionally, through gene annotation and expression pattern scrutiny, genes such as GAUT1, COP10, and DDB1 correlated with fruit traits in Capsicum frutescens and Capsicum annuum were validated via qRT-PCR. In the CH20 (Capsicum annuum) and YB-4 (Capsicum frutescens) cultivars, GAUT1 and COP10 were cloned with cDNA lengths of 1065 bp and 561 bp, respectively, exhibiting only a small number of single nucleotide variations and nucleotide deletions. This validation provides a robust reference for molecular marker-assisted breeding of pepper agronomic traits, offering both genetic resources and theoretical foundations for future endeavors in molecular marker-assisted breeding for pepper.

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References

Granat S, Wilson K, Tan-Wilson A . New serine carboxypeptidase in mung bean seedling cotyledons. J Plant Physiol. 2003; 160(10):1263-6. DOI: 10.1078/0176-1617-01128. View

Welch D, Hassan H, Blilou I, Immink R, Heidstra R, Scheres B . Arabidopsis JACKDAW and MAGPIE zinc finger proteins delimit asymmetric cell division and stabilize tissue boundaries by restricting SHORT-ROOT action. Genes Dev. 2007; 21(17):2196-204. PMC: 1950858. DOI: 10.1101/gad.440307. View

Gaedeke N, Klein M, Kolukisaoglu U, Forestier C, Muller A, Ansorge M . The Arabidopsis thaliana ABC transporter AtMRP5 controls root development and stomata movement. EMBO J. 2001; 20(8):1875-87. PMC: 125232. DOI: 10.1093/emboj/20.8.1875. View

-Chen J, Li W, Jia Y . The Serine Carboxypeptidase-Like Gene Negatively Regulates Membrane Lipid Metabolism in . Plants (Basel). 2020; 9(6). PMC: 7355682. DOI: 10.3390/plants9060696. View

Zhang C, Dong S, Xu J, He W, Yang T . PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files. Bioinformatics. 2018; 35(10):1786-1788. DOI: 10.1093/bioinformatics/bty875. View

Hwang I, Shin Y, Lee S, Lee J, Yoo S . Effects of Different Cooking Methods on the Antioxidant Properties of Red Pepper (Capsicum annuum L.). Prev Nutr Food Sci. 2014; 17(4):286-92. PMC: 3866734. DOI: 10.3746/pnf.2012.17.4.286. View

Chakrabarti M, Zhang N, Sauvage C, Munos S, Blanca J, Canizares J . A cytochrome P450 regulates a domestication trait in cultivated tomato. Proc Natl Acad Sci U S A. 2013; 110(42):17125-30. PMC: 3801035. DOI: 10.1073/pnas.1307313110. View

Sudre C, Goncalves L, Rodrigues R, do Amaral Junior A, Riva-Souza E, Bento C . Genetic variability in domesticated Capsicum spp as assessed by morphological and agronomic data in mixed statistical analysis. Genet Mol Res. 2010; 9(1):283-94. DOI: 10.4238/vol9-1gmr698. View

Alexander D, Novembre J, Lange K . Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 2009; 19(9):1655-64. PMC: 2752134. DOI: 10.1101/gr.094052.109. View

10.

Nimmakayala P, Abburi V, Saminathan T, Alaparthi S, Almeida A, Davenport B . Genome-wide Diversity and Association Mapping for Capsaicinoids and Fruit Weight in Capsicum annuum L. Sci Rep. 2016; 6:38081. PMC: 5128918. DOI: 10.1038/srep38081. View

11.

Chaim A, Borovsky Y, de Jong W, Paran I . Linkage of the A locus for the presence of anthocyanin and fs10.1, a major fruit-shape QTL in pepper. Theor Appl Genet. 2003; 106(5):889-94. DOI: 10.1007/s00122-002-1132-9. View

12.

Liu X, Lu H, Liu P, Miao H, Bai Y, Gu X . Identification of Novel Loci and Candidate Genes for Cucumber Downy Mildew Resistance Using GWAS. Plants (Basel). 2020; 9(12). PMC: 7768435. DOI: 10.3390/plants9121659. View

13.

Li Y, Fan C, Xing Y, Jiang Y, Luo L, Sun L . Natural variation in GS5 plays an important role in regulating grain size and yield in rice. Nat Genet. 2011; 43(12):1266-9. DOI: 10.1038/ng.977. View

14.

Chunthawodtiporn J, Hill T, Stoffel K, Van Deynze A . Quantitative Trait Loci Controlling Fruit Size and Other Horticultural Traits in Bell Pepper (). Plant Genome. 2018; 11(1). DOI: 10.3835/plantgenome2016.12.0125. View

15.

Kumar S, Stecher G, Li M, Knyaz C, Tamura K . MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Mol Biol Evol. 2018; 35(6):1547-1549. PMC: 5967553. DOI: 10.1093/molbev/msy096. View

16.

Visscher P, Brown M, McCarthy M, Yang J . Five years of GWAS discovery. Am J Hum Genet. 2012; 90(1):7-24. PMC: 3257326. DOI: 10.1016/j.ajhg.2011.11.029. View

17.

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

18.

Soyk S, Lemmon Z, Oved M, Fisher J, Liberatore K, Park S . Bypassing Negative Epistasis on Yield in Tomato Imposed by a Domestication Gene. Cell. 2017; 169(6):1142-1155.e12. DOI: 10.1016/j.cell.2017.04.032. View

19.

Pang Y, Liu C, Wang D, Amand P, Bernardo A, Li W . High-Resolution Genome-wide Association Study Identifies Genomic Regions and Candidate Genes for Important Agronomic Traits in Wheat. Mol Plant. 2020; 13(9):1311-1327. DOI: 10.1016/j.molp.2020.07.008. View

20.

Du H, Yang J, Chen B, Zhang X, Zhang J, Yang K . Target sequencing reveals genetic diversity, population structure, core-SNP markers, and fruit shape-associated loci in pepper varieties. BMC Plant Biol. 2019; 19(1):578. PMC: 6929450. DOI: 10.1186/s12870-019-2122-2. View