QTL Mapping and Improvement of Pre-harvest Sprouting Resistance Using Weedy Rice

Overview

Journal Front Plant Sci

Date 2023 Jun 21

PMID 37342139

Authors

Chang-Min Lee

Hyun-Su Park

Man-Kee Baek

O-Young Jeong

Jeonghwan Seo

Suk-Man Kim

Affiliations

Soon will be listed here.

Abstract

The stability of cultivation and production in terms of crop yield has been threatened by climate change due to global warming. Pre-harvest sprouting (PHS) is a threat to crops, especially staple foods, including rice, because of reductions in yield and quality. To address the problem of precocious germination before harvest, we performed quantitative trait loci (QTL) analysis for PHS using F RILs populations derived from weedy rice in Korea. QTL analysis revealed that two stable QTLs, and , associated with PHS resistance were identified on chromosomes 7 and 2, respectively, explaining approximately 38% of the phenotypic variation. The QTL effect in the tested lines significantly decreased the degree of PHS, based on the number of QTLs included. Through fine mapping for main QTL , the region for the PHS was found to be anchored within 23.575-23.785 Mbp on chromosome 7 using 13 cleaved amplified sequence (CAPS) markers. Among 15 open reading frames (ORFs) within the detected region, one ORF, Os07g0584366, exhibited upregulated expression in the resistant donor, which was approximately nine times higher than that of susceptible cultivars under PHS-inducing conditions. lines with QTLs related to PHS resistance were developed to improve the characteristics of PHS and design practical PCR-based DNA markers for marker-assisted backcrosses of many other PHS-susceptible cultivars.

Citing Articles

Comparative transcriptomes and WGCNA reveal hub genes for spike germination in different quinoa lines.

Huang L, Zhang L, Zhang P, Liu J, Li L, Li H BMC Genomics. 2024; 25(1):1231.

PMID: 39707180 PMC: 11662621. DOI: 10.1186/s12864-024-11151-y.

Molecular characteristics and expression pattern of the FAR1 gene during spike sprouting in quinoa.

Huang L, Zhang L, Zhang P, Liu J, Li L, Li H Sci Rep. 2024; 14(1):28485.

PMID: 39557968 PMC: 11573983. DOI: 10.1038/s41598-024-79474-0.

Genetic variation for tolerance to pre-harvest sprouting in mungbean () genotypes.

Gupta S, Aski M, Mishra G, Yadav P, Tripathi K, Lal S PeerJ. 2024; 12:e17609.

PMID: 39071133 PMC: 11276771. DOI: 10.7717/peerj.17609.

RicePilaf: a post-GWAS/QTL dashboard to integrate pangenomic, coexpression, regulatory, epigenomic, ontology, pathway, and text-mining information to provide functional insights into rice QTLs and GWAS loci.

Shrestha A, Gonzales M, Ong P, Larmande P, Lee H, Jeung J Gigascience. 2024; 13.

PMID: 38832465 PMC: 11148593. DOI: 10.1093/gigascience/giae013.

Genetic Enhancement of Cereals Using Genomic Resources for Nutritional Food Security.

Chaudhary N, Salgotra R, Chauhan B Genes (Basel). 2023; 14(9).

PMID: 37761910 PMC: 10530810. DOI: 10.3390/genes14091770.

References

Ye H, Feng J, Zhang L, Zhang J, Mispan M, Cao Z . Map-Based Cloning of Seed Dormancy1-2 Identified a Gibberellin Synthesis Gene Regulating the Development of Endosperm-Imposed Dormancy in Rice. Plant Physiol. 2015; 169(3):2152-65. PMC: 4634095. DOI: 10.1104/pp.15.01202. View

Cheon K, Won Y, Jeong Y, Lee Y, Kang D, Oh J . QTL mapping for pre-harvest sprouting resistance in japonica rice varieties utilizing genome re-sequencing. Mol Genet Genomics. 2020; 295(5):1129-1140. PMC: 7391406. DOI: 10.1007/s00438-020-01688-4. View

Gu X, Kianian S, Foley M . Multiple loci and epistases control genetic variation for seed dormancy in weedy rice (Oryza sativa). Genetics. 2004; 166(3):1503-16. PMC: 1470771. DOI: 10.1534/genetics.166.3.1503. View

Vetch J, Stougaard R, Martin J, Giroux M . Review: Revealing the genetic mechanisms of pre-harvest sprouting in hexaploid wheat (Triticum aestivum L.). Plant Sci. 2019; 281:180-185. DOI: 10.1016/j.plantsci.2019.01.004. View

Park S, Park H, Baek M, Jeong J, Cho Y, Lee G . Improving the Glossiness of Cooked Rice, an Important Component of Visual Rice Grain Quality. Rice (N Y). 2019; 12(1):87. PMC: 6881499. DOI: 10.1186/s12284-019-0348-0. View

Shao M, Bai G, Rife T, Poland J, Lin M, Liu S . QTL mapping of pre-harvest sprouting resistance in a white wheat cultivar Danby. Theor Appl Genet. 2018; 131(8):1683-1697. DOI: 10.1007/s00122-018-3107-5. View

Wei F, Droc G, Guiderdoni E, Hsing Y . International Consortium of Rice Mutagenesis: resources and beyond. Rice (N Y). 2013; 6(1):39. PMC: 3946042. DOI: 10.1186/1939-8433-6-39. View

Corbineau F, Xia Q, Bailly C, El-Maarouf-Bouteau H . Ethylene, a key factor in the regulation of seed dormancy. Front Plant Sci. 2014; 5:539. PMC: 4193209. DOI: 10.3389/fpls.2014.00539. View

Finkelstein R, Reeves W, Ariizumi T, Steber C . Molecular aspects of seed dormancy. Annu Rev Plant Biol. 2008; 59:387-415. DOI: 10.1146/annurev.arplant.59.032607.092740. View

10.

Lu Q, Niu X, Zhang M, Wang C, Xu Q, Feng Y . Genome-Wide Association Study of Seed Dormancy and the Genomic Consequences of Improvement Footprints in Rice ( L.). Front Plant Sci. 2018; 8:2213. PMC: 5760558. DOI: 10.3389/fpls.2017.02213. View

11.

Du L, Xu F, Fang J, Gao S, Tang J, Fang S . Endosperm sugar accumulation caused by mutation of PHS8/ISA1 leads to pre-harvest sprouting in rice. Plant J. 2018; 95(3):545-556. DOI: 10.1111/tpj.13970. View

12.

Jiang W, Lee J, Jin Y, Qiao Y, Piao R, Jang S . Identification of QTLs for seed germination capability after various storage periods using two RIL populations in rice. Mol Cells. 2011; 31(4):385-92. PMC: 3933968. DOI: 10.1007/s10059-011-0049-z. View

13.

Churchill G, Doerge R . Empirical threshold values for quantitative trait mapping. Genetics. 1994; 138(3):963-71. PMC: 1206241. DOI: 10.1093/genetics/138.3.963. View

14.

Shu K, Meng Y, Shuai H, Liu W, Du J, Liu J . Dormancy and germination: How does the crop seed decide?. Plant Biol (Stuttg). 2015; 17(6):1104-12. DOI: 10.1111/plb.12356. View

15.

Mizuno Y, Yamanouchi U, Hoshino T, Nonoue Y, Nagata K, Fukuoka S . Genetic dissection of pre-harvest sprouting resistance in an upland rice cultivar. Breed Sci. 2018; 68(2):200-209. PMC: 5982176. DOI: 10.1270/jsbbs.17062. View

16.

Lee J, Chebotarov D, McNally K, Pede V, Setiyono T, Raquid R . Novel Sources of Pre-Harvest Sprouting Resistance for Japonica Rice Improvement. Plants (Basel). 2021; 10(8). PMC: 8401653. DOI: 10.3390/plants10081709. View

17.

Wang L, Cheng J, Lai Y, Du W, Huang X, Wang Z . Identification of QTLs with additive, epistatic and QTL × development interaction effects for seed dormancy in rice. Planta. 2013; 239(2):411-20. DOI: 10.1007/s00425-013-1991-0. View

18.

Sohn S, Pandian S, Kumar T, Zoclanclounon Y, Muthuramalingam P, Shilpha J . Seed Dormancy and Pre-Harvest Sprouting in Rice-An Updated Overview. Int J Mol Sci. 2021; 22(21). PMC: 8583970. DOI: 10.3390/ijms222111804. View

19.

Tai L, Wang H, Xu X, Sun W, Ju L, Liu W . Pre-harvest sprouting in cereals: genetic and biochemical mechanisms. J Exp Bot. 2021; 72(8):2857-2876. DOI: 10.1093/jxb/erab024. View

20.

Liu S, Sehgal S, Li J, Lin M, Trick H, Yu J . Cloning and characterization of a critical regulator for preharvest sprouting in wheat. Genetics. 2013; 195(1):263-73. PMC: 3761307. DOI: 10.1534/genetics.113.152330. View