Fine mapping and candidate gene analysis of qHD5, a novel major QTL with pleiotropism for yield-related traits in rice (Oryza sativa L.).
A major QTL for heading date, qHD5, was fine-mapped to a 52.59-kb region on the short arm of rice chromosome 5. Heading date (HD) is one of the most important traits that enables rice to adapt to seasonal differences and specific growth conditions in diverse growing regions. In this study, a major-effect quantitative trait locus (QTL), qHD5, was resolved as a single Medelian factor that causes NIL(BG1) and NIL(XLJ) (two near-isogenic lines (NILs) used in our study) to have at a minimum of 10-day difference in HD under both long-day and short-day conditions in rice. qHD5 was initially mapped to a 309.52-kb genomic region in our previous study. Here, using an advanced BC4F3population and map-based cloning, we further narrowed the location of qHD5 to a 52.59-kb region between the H71 and RD502 markers. Sequence analysis revealed that Os05g03040, which putatively encodes an AP2(APETALA2) transcription factor, has six single nucleotide polymorphisms (SNPs) between NIL(BG1) and NIL(XLJ). On this basis, this gene was concluded to be the most probable candidate gene for qHD5. Our results also showed that Hd3a, RFT1, Hd1, Ehd1, and Ghd7 were differentially expressed in the two NILs. Moreover, qHD5 was found to affect yield-related traits such as flag leaf width, flag leaf length, branch number, and 1000-grain weight.
Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China.|State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
Bin
B
Sun
Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China.|State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
Xiao-Deng
XD
Zhan
Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China.|State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
Ze-Chuan
ZC
Lin
Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China.|State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
Wei-Xun
WX
Wu
Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China.|State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
Ping
P
Yu
Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China.|State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
Ying-Xin
YX
Zhang
Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China.|State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
Lian-Ping
LP
Sun
Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China. caolycgf@mail.hz.zj.cn.|State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China. caolycgf@mail.hz.zj.cn.
Li-Yong
LY
Cao
Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China. shcheng@mail.hz.zj.cn.|State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China. shcheng@mail.hz.zj.cn.
Shi-Hua
SH
Cheng
D002874:Chromosome Mapping; D018744:DNA, Plant / Q000235:genetics; D002523:Edible Grain / Q000235:genetics*; D017343:Genes, Plant; D058685:Genetic Pleiotropy; D012275:Oryza / Q000235:genetics*; D010641:Phenotype; D017440:Photoperiod; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D017422:Sequence Analysis, DNA
D018744:DNA, Plant
Planta. 2008 Jul;228(2):355-65
18449564
Theor Appl Genet. 2015 Jun;128(6):1073-82
25748116
Rice (N Y). 2014 Dec;7(1):31
26224560
Genes Dev. 2015 May 1;29(9):975-87
25934507
Plant Cell. 1994 Oct;6(10):1343-1355
12244224
Plant Cell. 2000 Dec;12(12):2473-2484
11148291
Genes Dev. 2004 Apr 15;18(8):926-36
15078816
Plant Cell Rep. 2011 Dec;30(12):2243-54
21830130
Theor Appl Genet. 2013 Mar;126(3):611-8
23090144
Nat Genet. 2008 Jun;40(6):761-7
18454147
PLoS One. 2013 Oct 01;8(10):e75959
24098411
Plant J. 2013 Oct;76(1):36-46
23789941
Proc Natl Acad Sci U S A. 2007 Jul 3;104(27):11376-81
17595297
Methods. 2001 Dec;25(4):402-8
11846609
Plant Cell. 2003 Nov;15(11):2730-41
14555699
Nucleic Acids Res. 1980 Oct 10;8(19):4321-5
7433111
FEBS Lett. 2009 Jul 7;583(13):2165-70
19508870
PLoS Genet. 2013;9(2):e1003281
23437005
Plant Physiol. 2010 Aug;153(4):1747-58
20566706
Plant Sci. 2014 Feb;215-216:29-38
24388512
Genes Dev. 1998 Apr 15;12(8):1145-54
9553044
Plant J. 2010 Dec;64(6):936-47
21143675
Proc Natl Acad Sci U S A. 2001 Jul 3;98(14):7922-7
11416158
Plant J. 2007 Jan;49(1):64-78
17144896
Theor Appl Genet. 2003 Nov;107(7):1174-80
12898024
Plant J. 2015 Apr;82(2):256-66
25740115
Proc Natl Acad Sci U S A. 2014 Nov 18;111(46):16337-42
25378698
J Plant Physiol. 2009 Nov 1;166(16):1801-13
19560230
Plant Cell Physiol. 2011 Jun;52(6):1083-94
21565907
Planta. 2009 May;229(6):1159-69
19198875
Plant Mol Biol. 2014 Feb;84(3):301-14
24132771
Plant J. 2011 May;66(4):603-12
21284756
Plant Cell Physiol. 2012 Apr;53(4):709-16
22399582
Plant Cell Physiol. 2002 Oct;43(10):1096-105
12407188
J Biol Chem. 2003 Apr 18;278(16):14306-12
12562764
Mol Plant. 2013 Nov;6(6):1877-88
23713079
Theor Appl Genet. 2014 Nov;127(11):2515-24
25223543
Plant Biol (Stuttg). 2015 May;17(3):599-607
25280352
Plant J. 2012 Feb;69(3):445-61
22003982
Gene. 2015 Oct 25;571(2):263-70
26123916
PLoS Biol. 2009 Jul;7(7):e1000148
19582143
Genetics. 2003 May;164(1):311-21
12750342
Proc Natl Acad Sci U S A. 1997 Jun 24;94(13):7076-81
9192694
Plant Physiol. 2001 Dec;127(4):1425-9
11743085
Proc Natl Acad Sci U S A. 2013 Feb 19;110(8):2775-80
23388640