QTL mapping and improvement of pre-harvest sprouting resistance using <i>japonica</i> weedy rice

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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 ₈ RILs populations derived from japonica weedy rice in Korea. QTL analysis revealed that two stable QTLs, qPH7 and qPH2, 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 qPH7, 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 japonica cultivars under PHS-inducing conditions. Japonica 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 japonica cultivars.

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Most cited references 44

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QTL IciMapping: Integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations

Lei Meng, Huihui Li, Luyan Zhang … (2015)

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Molecular aspects of seed dormancy.

Ruth Finkelstein, Wendy Reeves, Tohru Ariizumi … (2008)

Seed dormancy provides a mechanism for plants to delay germination until conditions are optimal for survival of the next generation. Dormancy release is regulated by a combination of environmental and endogenous signals with both synergistic and competing effects. Molecular studies of dormancy have correlated changes in transcriptomes, proteomes, and hormone levels with dormancy states ranging from deep primary or secondary dormancy to varying degrees of release. The balance of abscisic acid (ABA):gibberellin (GA) levels and sensitivity is a major, but not the sole, regulator of dormancy status. ABA promotes dormancy induction and maintenance, whereas GA promotes progression from release through germination; environmental signals regulate this balance by modifying the expression of biosynthetic and catabolic enzymes. Mediators of environmental and hormonal response include both positive and negative regulators, many of which are feedback-regulated to enhance or attenuate the response. The net result is a slightly heterogeneous response, thereby providing more temporal options for successful germination.

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Empirical threshold values for quantitative trait mapping.

G Churchill, R. W. Doerge (1994)

The detection of genes that control quantitative characters is a problem of great interest to the genetic mapping community. Methods for locating these quantitative trait loci (QTL) relative to maps of genetic markers are now widely used. This paper addresses an issue common to all QTL mapping methods, that of determining an appropriate threshold value for declaring significant QTL effects. An empirical method is described, based on the concept of a permutation test, for estimating threshold values that are tailored to the experimental data at hand. The method is demonstrated using two real data sets derived from F(2) and recombinant inbred plant populations. An example using simulated data from a backcross design illustrates the effect of marker density on threshold values.

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Author and article information

Contributors

Chang-Min Lee: URI : https://loop.frontiersin.org/people/2264488

Jeonghwan Seo: URI : https://loop.frontiersin.org/people/551711

Suk-Man Kim: URI : https://loop.frontiersin.org/people/1853105

Journal

Journal ID (nlm-ta): Front Plant Sci

Journal ID (iso-abbrev): Front Plant Sci

Journal ID (publisher-id): Front. Plant Sci.

Title: Frontiers in Plant Science

Publisher: Frontiers Media S.A.

ISSN (Electronic): 1664-462X

Publication date (Electronic): 05 June 2023

Publication date Collection: 2023

Volume: 14

Electronic Location Identifier: 1194058

Affiliations

[1] ¹ Crop Breeding Division, National Institute of Crop Science , Rural Development Administration, Wanju, Republic of Korea

[2] ² Department of Ecological & Environmental System, Kyungpook National University , Sangju, Republic of Korea

Author notes

Edited by: Peterson Wambugu, Kenya Agricultural and Livestock Research Organization, Kenya

Reviewed by: Longzhi Han, Chinese Academy of Agricultural Sciences (CAAS), China; Yawen Zeng, Yunnan Academy of Agricultural Sciences, China

*Correspondence: Suk-Man Kim, s_kim@ 123456knu.ac.kr

†ORCID: Suk-Man Kim, orcid.org/0000-0002-6701-4824; Chang-Min Lee, orcid.org/0000-0001-9562-2715; Jeonghwan Seo, orcid.org/0000-0003-1740-5058

Article

DOI: 10.3389/fpls.2023.1194058

PMC ID: 10277695

PubMed ID: 37342139

SO-VID: 52e05d72-022f-40ca-9ea7-ecb1cdca4167

License:

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

History

Date received : 26 March 2023

Date accepted : 25 April 2023

Page count

Figures: 5, Tables: 3, Equations: 0, References: 44, Pages: 9, Words: 5073

Funding

Funded by: Rural Development Administration , doi 10.13039/501100003627;

This work was carried out with the support of the Cooperative Research Program for Agricultural Science & Technology Development (“A study on the resistance of breeding materials to environmental stresses originating from Korean native resources”) (project no. PJ01480402), Rural Development Administration, Republic of Korea.

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section-in-acceptance Plant Breeding

ScienceOpen disciplines: Plant science & Botany

Keywords: rice,pre-harvest sprouting (phs),quantitative trait loci (qtl),germination,dormancy

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ScienceOpen disciplines: Plant science & Botany

Keywords: rice, pre-harvest sprouting (phs), quantitative trait loci (qtl), germination, dormancy

QTL mapping and improvement of pre-harvest sprouting resistance using japonica weedy rice

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Climate Change: Open Access

Most cited references 44

QTL IciMapping: Integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations

Molecular aspects of seed dormancy.

Empirical threshold values for quantitative trait mapping.

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