Genetic Dissection of Agronomically Important Traits in Closely Related Temperate Rice Cultivars

Overview

Journal Breed Sci

Date 2018 Feb 6

PMID 29398936

Citations 7

Authors

Kiyosumi Hori

Toshio Yamamoto

Masahiro Yano

Affiliations

Soon will be listed here.

Abstract

Many quantitative trait loci (QTLs) for agronomically important traits such as grain yield, disease resistance, and stress tolerance of rice ( L.) have been detected by using segregating populations derived from crosses between and subspecies or with wild relatives. However, the QTLs involved in the control of natural variation in agronomic traits among closely related cultivars are still unclear. Decoding the whole genome sequences of Nipponbare and other temperate rice cultivars has accelerated the collection of a huge number of single nucleotide polymorphisms (SNPs). These SNPs are good resource for developing polymorphic DNA markers and for detecting QTLs distributed across all rice chromosomes. The temperate rice cultivar Koshihikari has remained the top cultivar for about 40 years since 1979 in Japan. Unraveling the genetic factors in Koshihikari will provide important insights into improving agronomic traits in temperate rice cultivars. Here we describe recent progress in our studies as an example of genetic analysis in closely related cultivars.

Citing Articles

Rice ( L.) Grain Size, Shape, and Weight-Related QTLs Identified Using GWAS with Multiple GAPIT Models and High-Density SNP Chip DNA Markers.

Kabange N, Dzorkpe G, Park D, Kwon Y, Lee S, Lee S Plants (Basel). 2023; 12(23).

PMID: 38068684 PMC: 10708019. DOI: 10.3390/plants12234044.

Characterization and QTL Mapping of a Major Field Resistance Locus for Bacterial Blight in Rice.

Park J, Lee C, Ji H, Baek M, Seo J, Jeong O Plants (Basel). 2022; 11(11).

PMID: 35684177 PMC: 9182613. DOI: 10.3390/plants11111404.

Development and characterization of chromosome segment substitution lines derived from backcross between donor rice cultivar Yukihikari and recipient cultivar Kirara397.

Kato K, Hirayama Y Breed Sci. 2021; 71(2):283-290.

PMID: 34377077 PMC: 8329885. DOI: 10.1270/jsbbs.20128.

Development of 454 New Kompetitive Allele-Specific PCR (KASP) Markers for Temperate Rice Varieties.

Cheon K, Jeong Y, Oh H, Oh J, Kang D, Kim N Plants (Basel). 2020; 9(11).

PMID: 33182649 PMC: 7698039. DOI: 10.3390/plants9111531.

QTL mapping for pre-harvest sprouting resistance in japonica rice varieties utilizing genome re-sequencing.

Cheon K, Won Y, Jeong Y, Lee Y, Kang D, Oh J Mol Genet Genomics. 2020; 295(5):1129-1140.

PMID: 32458040 PMC: 7391406. DOI: 10.1007/s00438-020-01688-4.

References

Hori K, Matsubara K, Yano M . Genetic control of flowering time in rice: integration of Mendelian genetics and genomics. Theor Appl Genet. 2016; 129(12):2241-2252. DOI: 10.1007/s00122-016-2773-4. View

Takagi H, Tamiru M, Abe A, Yoshida K, Uemura A, Yaegashi H . MutMap accelerates breeding of a salt-tolerant rice cultivar. Nat Biotechnol. 2015; 33(5):445-9. DOI: 10.1038/nbt.3188. View

Nagata K, Ando T, Nonoue Y, Mizubayashi T, Kitazawa N, Shomura A . Advanced backcross QTL analysis reveals complicated genetic control of rice grain shape in a japonica × indica cross. Breed Sci. 2015; 65(4):308-18. PMC: 4542931. DOI: 10.1270/jsbbs.65.308. View

Huang X, Zhao Y, Wei X, Li C, Wang A, Zhao Q . Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm. Nat Genet. 2011; 44(1):32-9. DOI: 10.1038/ng.1018. View

Hori K, Nonoue Y, Ono N, Shibaya T, Ebana K, Matsubara K . Genetic architecture of variation in heading date among Asian rice accessions. BMC Plant Biol. 2015; 15:115. PMC: 4424449. DOI: 10.1186/s12870-015-0501-x. View

Hori K, Ogiso-Tanaka E, Matsubara K, Yamanouchi U, Ebana K, Yano M . Hd16, a gene for casein kinase I, is involved in the control of rice flowering time by modulating the day-length response. Plant J. 2013; 76(1):36-46. PMC: 4223384. DOI: 10.1111/tpj.12268. View

Hori K, Sugimoto K, Nonoue Y, Ono N, Matsubara K, Yamanouchi U . Detection of quantitative trait loci controlling pre-harvest sprouting resistance by using backcrossed populations of japonica rice cultivars. Theor Appl Genet. 2010; 120(8):1547-57. PMC: 2859223. DOI: 10.1007/s00122-010-1275-z. View

Kovach M, Calingacion M, Fitzgerald M, McCouch S . The origin and evolution of fragrance in rice (Oryza sativa L.). Proc Natl Acad Sci U S A. 2009; 106(34):14444-9. PMC: 2732888. DOI: 10.1073/pnas.0904077106. View

Matsubara K, Kono I, Hori K, Nonoue Y, Ono N, Shomura A . Novel QTLs for photoperiodic flowering revealed by using reciprocal backcross inbred lines from crosses between japonica rice cultivars. Theor Appl Genet. 2008; 117(6):935-45. DOI: 10.1007/s00122-008-0833-0. View

10.

Asano K, Yamasaki M, Takuno S, Miura K, Katagiri S, Ito T . Artificial selection for a green revolution gene during japonica rice domestication. Proc Natl Acad Sci U S A. 2011; 108(27):11034-9. PMC: 3131315. DOI: 10.1073/pnas.1019490108. View

11.

Schaeffer L . Strategy for applying genome-wide selection in dairy cattle. J Anim Breed Genet. 2006; 123(4):218-23. DOI: 10.1111/j.1439-0388.2006.00595.x. View

12.

Matsubara K, Hori K, Ogiso-Tanaka E, Yano M . Cloning of quantitative trait genes from rice reveals conservation and divergence of photoperiod flowering pathways in Arabidopsis and rice. Front Plant Sci. 2014; 5:193. PMC: 4026727. DOI: 10.3389/fpls.2014.00193. View

13.

Mahender A, Anandan A, Pradhan S . Early seedling vigour, an imperative trait for direct-seeded rice: an overview on physio-morphological parameters and molecular markers. Planta. 2015; 241(5):1027-50. DOI: 10.1007/s00425-015-2273-9. View

14.

Fujino K, Sekiguchi H, Matsuda Y, Sugimoto K, Ono K, Yano M . Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice. Proc Natl Acad Sci U S A. 2008; 105(34):12623-8. PMC: 2527961. DOI: 10.1073/pnas.0805303105. View

15.

Shibaya T, Nonoue Y, Ono N, Yamanouchi U, Hori K, Yano M . Genetic interactions involved in the inhibition of heading by heading date QTL, Hd2 in rice under long-day conditions. Theor Appl Genet. 2011; 123(7):1133-43. DOI: 10.1007/s00122-011-1654-0. View

16.

Famoso A, Zhao K, Clark R, Tung C, Wright M, Bustamante C . Genetic architecture of aluminum tolerance in rice (Oryza sativa) determined through genome-wide association analysis and QTL mapping. PLoS Genet. 2011; 7(8):e1002221. PMC: 3150440. DOI: 10.1371/journal.pgen.1002221. View

17.

Yonemaru J, Yamamoto T, Ebana K, Yamamoto E, Nagasaki H, Shibaya T . Genome-wide haplotype changes produced by artificial selection during modern rice breeding in Japan. PLoS One. 2012; 7(3):e32982. PMC: 3302797. DOI: 10.1371/journal.pone.0032982. View

18.

Takeuchi Y, Lin S, Sasaki T, Yano M . Fine linkage mapping enables dissection of closely linked quantitative trait loci for seed dormancy and heading in rice. Theor Appl Genet. 2003; 107(7):1174-80. DOI: 10.1007/s00122-003-1364-3. View

19.

Xu F, Bao J, He Q, Park Y . Genome-wide association study of eating and cooking qualities in different subpopulations of rice (Oryza sativa L.). BMC Genomics. 2016; 17:663. PMC: 4992570. DOI: 10.1186/s12864-016-3000-z. View

20.

Yamamoto T, Nagasaki H, Yonemaru J, Ebana K, Nakajima M, Shibaya T . Fine definition of the pedigree haplotypes of closely related rice cultivars by means of genome-wide discovery of single-nucleotide polymorphisms. BMC Genomics. 2010; 11:267. PMC: 2874813. DOI: 10.1186/1471-2164-11-267. View