GWAS and Meta-QTL Analysis of Kernel Quality-Related Traits in Maize

Overview

Journal Plants (Basel)

Date 2024 Oct 16

PMID 39409600

Authors

Rui Tang

Zelong Zhuang

Jianwen Bian

Zhenping Ren

Wanling Ta

Yunling Peng

Affiliations

Soon will be listed here.

Abstract

The quality of corn kernels is crucial for their nutritional value, making the enhancement of kernel quality a primary objective of contemporary corn breeding efforts. This study utilized 260 corn inbred lines as research materials and assessed three traits associated with grain quality. A genome-wide association study (GWAS) was conducted using the best linear unbiased estimator (BLUE) for quality traits, resulting in the identification of 23 significant single nucleotide polymorphisms (SNPs). Additionally, nine genes associated with grain quality traits were identified through gene function annotation and prediction. Furthermore, a total of 697 quantitative trait loci (QTL) related to quality traits were compiled from 27 documents, followed by a meta-QTL analysis that revealed 40 meta-QTL associated with these traits. Among these, 19 functional genes and reported candidate genes related to quality traits were detected. Three significant SNPs identified by GWAS were located within the intervals of these QTL, while the remaining eight significant SNPs were situated within 2 Mb of the QTL. In summary, the findings of this study provide a theoretical framework for analyzing the genetic basis of corn grain quality-related traits and for enhancing corn quality.

References

Li H, Peng Z, Yang X, Wang W, Fu J, Wang J . Genome-wide association study dissects the genetic architecture of oil biosynthesis in maize kernels. Nat Genet. 2012; 45(1):43-50. DOI: 10.1038/ng.2484. View

Liu B, Yang D, Wang D, Liang C, Wang J, Lisch D . Heritable changes of epialleles near genes in maize can be triggered in the absence of CHH methylation. Plant Physiol. 2023; 194(4):2511-2532. PMC: 10980416. DOI: 10.1093/plphys/kiad668. View

Arriagada O, Arevalo B, Cabeza R, Carrasco B, Schwember A . Meta-QTL Analysis for Yield Components in Common Bean ( L.). Plants (Basel). 2023; 12(1). PMC: 9824219. DOI: 10.3390/plants12010117. View

Maghraby A, Alzalaty M . Genome-wide identification and evolutionary analysis of the AP2/EREBP, COX and LTP genes in Zea mays L. under drought stress. Sci Rep. 2024; 14(1):7610. PMC: 10982304. DOI: 10.1038/s41598-024-57376-5. View

Ogunyemi A, Otegbayo B, Fagbenro J . Effects of NPK and biochar fertilized soil on the proximate composition and mineral evaluation of maize flour. Food Sci Nutr. 2019; 6(8):2308-2313. PMC: 6563416. DOI: 10.1002/fsn3.808. View

Xie S, Luo H, Huang W, Jin W, Dong Z . Striking a growth-defense balance: Stress regulators that function in maize development. J Integr Plant Biol. 2023; 66(3):424-442. DOI: 10.1111/jipb.13570. View

Li H, Li Y, Wang X, Jiao Z, Zhang W, Long Y . Characterization of Glycosyltransferase Family 1 (GT1) and Their Potential Roles in Anthocyanin Biosynthesis in Maize. Genes (Basel). 2023; 14(11). PMC: 10671782. DOI: 10.3390/genes14112099. View

Welcker C, Sadok W, Dignat G, Renault M, Salvi S, Charcosset A . A common genetic determinism for sensitivities to soil water deficit and evaporative demand: meta-analysis of quantitative trait Loci and introgression lines of maize. Plant Physiol. 2011; 157(2):718-29. PMC: 3192567. DOI: 10.1104/pp.111.176479. View

Cheng C, An L, Li F, Ahmad W, Aslam M, Zia Ul Haq M . Wide-Range Portrayal of AP2/ERF Transcription Factor Family in Maize ( L.) Development and Stress Responses. Genes (Basel). 2023; 14(1). PMC: 9859492. DOI: 10.3390/genes14010194. View

10.

Cook J, McMullen M, Holland J, Tian F, Bradbury P, Ross-Ibarra J . Genetic architecture of maize kernel composition in the nested association mapping and inbred association panels. Plant Physiol. 2011; 158(2):824-34. PMC: 3271770. DOI: 10.1104/pp.111.185033. View

11.

Zhang S, Wu S, Hou Q, Zhao J, Fang C, An X . Fatty acid de novo biosynthesis in plastids: Key enzymes and their critical roles for male reproduction and other processes in plants. Plant Physiol Biochem. 2024; 210:108654. DOI: 10.1016/j.plaphy.2024.108654. View

12.

Niu L, Liu L, Zhang J, Scali M, Wang W, Hu X . Genetic Engineering of Starch Biosynthesis in Maize Seeds for Efficient Enzymatic Digestion of Starch during Bioethanol Production. Int J Mol Sci. 2023; 24(4). PMC: 9967003. DOI: 10.3390/ijms24043927. View

13.

Hu S, Wang M, Zhang X, Chen W, Song X, Fu X . Genetic basis of kernel starch content decoded in a maize multi-parent population. Plant Biotechnol J. 2021; 19(11):2192-2205. PMC: 8541773. DOI: 10.1111/pbi.13645. View

14.

Sethi M, Singh A, Kaur H, Phagna R, Rakshit S, Chaudhary D . Expression profile of protein fractions in the developing kernel of normal, Opaque-2 and quality protein maize. Sci Rep. 2021; 11(1):2469. PMC: 7844038. DOI: 10.1038/s41598-021-81906-0. View

15.

Li W, Li Y, Shi H, Wang H, Ji K, Zhang L . ZmMPK6, a mitogen-activated protein kinase, regulates maize kernel weight. J Exp Bot. 2024; 75(11):3287-3299. DOI: 10.1093/jxb/erae104. View

16.

Shen B, Allen W, Zheng P, Li C, Glassman K, Ranch J . Expression of ZmLEC1 and ZmWRI1 increases seed oil production in maize. Plant Physiol. 2010; 153(3):980-7. PMC: 2899924. DOI: 10.1104/pp.110.157537. View

17.

Zheng Y, Yuan F, Huang Y, Zhao Y, Jia X, Zhu L . Genome-wide association studies of grain quality traits in maize. Sci Rep. 2021; 11(1):9797. PMC: 8105333. DOI: 10.1038/s41598-021-89276-3. View

18.

Yang G, Dong Y, Li Y, Wang Q, Shi Q, Zhou Q . Verification of QTL for grain starch content and its genetic correlation with oil content using two connected RIL populations in high-oil maize. PLoS One. 2013; 8(1):e53770. PMC: 3540064. DOI: 10.1371/journal.pone.0053770. View

19.

Ng D, Wang T, Chandrasekharan M, Aramayo R, Kertbundit S, Hall T . Plant SET domain-containing proteins: structure, function and regulation. Biochim Biophys Acta. 2007; 1769(5-6):316-29. PMC: 2794661. DOI: 10.1016/j.bbaexp.2007.04.003. View

20.

Liu N, Xue Y, Guo Z, Li W, Tang J . Genome-Wide Association Study Identifies Candidate Genes for Starch Content Regulation in Maize Kernels. Front Plant Sci. 2016; 7:1046. PMC: 4961707. DOI: 10.3389/fpls.2016.01046. View