Mapping of QTLs for Tolerance of Hypoxia Germination in Rice with a High-density Genetic Map

Xiaoxia YAN; Manshan ZHU; Feng WANG; Wuge LIU; Jinhua LI; Xing HUO; Yongxiang HUANG; Dilin LIU

doi:10.16768/j.issn.1004-874X.2023.04.002

Guangdong nongye kexue (Apr 2023)

Mapping of QTLs for Tolerance of Hypoxia Germination in Rice with a High-density Genetic Map

Xiaoxia YAN,
Manshan ZHU,
Feng WANG,
Wuge LIU,
Jinhua LI,
Xing HUO,
Yongxiang HUANG,
Dilin LIU

Affiliations

Xiaoxia YAN: College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
Manshan ZHU: Rice Research Institute, Guangdong Academy of Agricultural Sciences / Guangdong Key Laboratory of New Technology in Rice Breeding / Guangdong Rice Engineering Laboratory / Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
Feng WANG: Rice Research Institute, Guangdong Academy of Agricultural Sciences / Guangdong Key Laboratory of New Technology in Rice Breeding / Guangdong Rice Engineering Laboratory / Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
Wuge LIU: Rice Research Institute, Guangdong Academy of Agricultural Sciences / Guangdong Key Laboratory of New Technology in Rice Breeding / Guangdong Rice Engineering Laboratory / Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
Jinhua LI: Rice Research Institute, Guangdong Academy of Agricultural Sciences / Guangdong Key Laboratory of New Technology in Rice Breeding / Guangdong Rice Engineering Laboratory / Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
Xing HUO: Rice Research Institute, Guangdong Academy of Agricultural Sciences / Guangdong Key Laboratory of New Technology in Rice Breeding / Guangdong Rice Engineering Laboratory / Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
Yongxiang HUANG: College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
Dilin LIU: Rice Research Institute, Guangdong Academy of Agricultural Sciences / Guangdong Key Laboratory of New Technology in Rice Breeding / Guangdong Rice Engineering Laboratory / Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China

DOI: https://doi.org/10.16768/j.issn.1004-874X.2023.04.002
Journal volume & issue: Vol. 50, no. 4
pp. 13 – 21

Abstract

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【Objective】Tolerance to hypoxia germination is one of the key traits for direct-seeding adaptability of rice. The temperate direct-seeding japonica rice variety Francis and multi-panicle indica restorer line R998 were used for QTL mapping of hypoxia germination related traits, aiming to provide new valuable gene resources for developing direct-seeding rice varieties and the promotion of direct-seeding rice production methods.【Method】The coleoptile length, shoot length and maximum root length of rice seedlings submerged in 10-cm-depth water in the dark for 7 days at 28℃ were recorded as indicators of hypoxia germination tolerance capacity. A high-density genetic map containing 3 106 bin markers was constructed by low-coverage genome re-sequencing, and QTL scanning was performed with WinQTL Cart 2.5.【Result】Under the condition of hypoxia germination, the coleoptile length and root length of Francis are significantly higher than those of R998, but there is no significant difference in shoot length between them. The total genetic distance of the constructed genetic map is 3 646.2 cM, in which the number of markers on chromosome 12 is the least, and that on chromosome 1 is the most, with 174 and 389, respectively. The average marker distance in the genetic map is 1.21 cM, the marker distance of each chromosomes is 0.68 -1.84 cM, and the gaps above 5 cM account for 0.36%. By using composite interval mapping (CIM), six QTLs related to hypoxia germination tolerance are detected on 5 chromosomes. Among them, the number of QTLs controlling coleoptile length, shoot length and root length are 3, 1 and 2, respectively. The coleoptile locus qCL9 and the shoot length locus qSL5 had a phenotypic variance explained (PVE) over 10%, which are 13.39% and 10.78%, respectively. The beneficial allele of qCL9 and the root length locus qRL2-1 come from the parent Francis, while the other four beneficial alleles are provided by the parent R998. Three of the six QTLs have not been reported previously, therefore, they may be novel QTLs.【Conclusion】In summary, there is significant difference between Francis and R998 in hypoxia germination, and both parents have beneficial alleles for hypoxia germination tolerance. qCL9 and qSL5 are major effect QTLs controlling hypoxia germination tolerance and have practical value in the molecular breeding of direct-seeding rice.

Published in Guangdong nongye kexue

ISSN: 1004-874X (Print)
Publisher: Guangdong Academy of Agricultural Sciences
Country of publisher: China
LCC subjects: Agriculture
Website: http://gdnykx.cnjournals.org/gdnykx/ch/index.aspx

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