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Acta Agronomica Sinica ›› 2023, Vol. 49 ›› Issue (1): 119-128.doi: 10.3724/SP.J.1006.2023.12089


Mapping of QTLs for heading date of rice with high-density bin genetic map

ZHAO Ling(), LIANG Wen-Hua, ZHAO Chun-Fang, WEI Xiao-Dong, ZHOU Li-Hui, YAO Shu, WANG Cai-Lin, ZHANG Ya-Dong()   

  1. Institute of Food Crops, Jiangsu Academy of Agricultural Sciences / Nanjing Branch of China National Center for Rice Improvement / East China Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice / Jiangsu High Quality Rice Research & Development Center, Nanjing 210014, Jiangsu, China
  • Received:2021-12-28 Accepted:2022-05-05 Online:2023-01-12 Published:2022-05-13
  • Contact: ZHANG Ya-Dong E-mail:zhaoling@jaas.ac.cn;zhangyd@jaas.ac.cn
  • Supported by:
    Jiangsu Science and Technology Development Program(BE2019375)


Identification of new loci and genes related to heading date is very important for the genetic mechanism research and molecular improvement in rice. A recombinant inbred lines (RILs) was developed by crossing the japonica rice TD70 and the indica rice Kasalath with obvious difference in heading date. A high-density genetic linkage map with 12,328 recombination Bin markers was constructed based on the re-sequencing data of parents and RILs. The RILs and two parents were planted at the Jiangsu Academy of Agricultural Sciences, in Nanjing in 2018 and 2021. QTLs that controlled the heading date were analyzed by IciMappingv3.4 software with inclusive compound interval mapping method. 15 QTLs related to heading date of rice were detected, distributed on chromosome 3, 6, 7, 8, 10, and 12 in two years. The phenotype variation explained (PVE) and LOD value of single QTL ranged from 3.29%-14.73% and 2.58-10.68, respectively. Among them, seven QTLs were found to locate in the same interval or adjacent to previously QTLs, and four QTLs were detected in two years indicating their genetic stability. According to the annotation and sequences analysis of genes located in the region of repeatable QTLs, we found that seven annotated genes had non-synonymous mutations in the coding regions between TD70 and Kasalath. Based on the mutations in the coding regions, the haplotypes of seven genes were identified in RIL population. The heading date of RILs had significant difference between the RILs with different haplotype of four genes, indicating that they might be the candidate genes for heading date. These results could be useful for subsequent functional studies and molecular marker assisted breeding of heading date.

Key words: rice (Oryza sativa L.), recombinant inbred lines, high-density bin map, heading date, QTLs

Fig. 1

Distribution of heading dates in the RIL population K: Kasalath; T: TD70."

Table 1

Heading date among the RIL population and two parents"

年份Year 亲本Parents (d) 重组自交系RIL population
TD70 Kasalath 平均值Average (d) 变异范围
CV (%)
2018 106 84 98.6 85-117 5.23 -0.73 0.28
2021 99 89 96.5 84-111 7.55 0.08 0.14

Table 2

Identification of QTL contributing to heading date in RIL population"

年份Year QTL 染色体Chr. 标记区间
Marker interval
Confidence interval (Mb)
LOD 贡献率
PVE (%)
Additive effect
2018 qHD3 3 RBN2916-RBN2917 21.75-21.81 2.58 3.29 1.41
qHD6.1 6 RBN5492-RBN5493 1.80-1.85 10.68 14.73 2.98
qHD6.2 6 RBN5834-RBN5835 10.93-11.07 3.15 4.65 -2.58
qHD7.1* 7 RBN7031-RBN7032 14.50-14.54 6.02 11.77 2.66
qHD7.2 7 RBN7535-RBN7536 28.65-28.71 3.73 4.77 -1.70
qHD8* 8 RBN7647-RBN7648 1.73-1.82 3.11 3.97 1.56
qHD10.1* 10 RBN9497-RBN9498 3.15-3.20 4.89 6.30 2.40
qHD10.2* 10 RBN9520-RBN9521 3.61-3.71 6.01 10.19 2.36
2021 qHD7.1* 7 RBN7031-RBN7032 14.50-14.54 8.21 12.58 1.81
qHD7.3 7 RBN6705-RBN6706 4.47-4.52 7.84 11.80 1.74
qHD7.4 7 RBN7524-RBN7525 28.35-28.37 6.27 9.66 -1.58
qHD8* 8 RBN7647-RBN7648 1.73-1.82 3.15 3.92 1.01
qHD10.1* 10 RBN9497-RBN9498 3.15-3.20 4.95 6.52 1.32
qHD10.2* 10 RBN9520-RBN9521 3.61-3.71 4.06 6.24 1.53
qHD12 12 RBN12280-RBN12281 26.21-26.27 3.06 4.47 1.07

Fig. 2

Distribution of QTLs contributing to heading date on chromosomes"

Table 3

Annotated genes in interval of repeat QTLs"

QTL 染色体
物理图谱区间Interval (Mb) 基因
Gene name
Gene annotation
qHD7.1 7 14.50-14.54 Os07g0434500 SNF2家族蛋白 Snf2 family protein
Os07g0434700* 甲硫氨酸氨基肽酶家族成员 Methionine aminopeptidase family protein
Os07g0435100 26S蛋白酶体非ATP酶调节亚基8
26S proteasome non-ATPase regulatory subunit 8
Os07g0435300 光系统I反应中心亚基IV A, 叶绿体前体
Photosystem I reaction center subunit IV A, chloroplast precursor
Os07g0435400 WD结构域, G-β重复结构域蛋白
WD domain, G-beta repeat domain containing protein
qHD8 8 1.73-1.82 Os08g0130900* 半乳糖基转移酶家族 Galactosyltransferase family
Os08g0131000 五肽 Pentatricopeptide
Os08g0131100* 细胞色素P450羟化酶 Cytochrome P450 hydroxylase
Os08g0131200 蛋白酶抑制剂, 种子储存, LTP家族蛋白前体
Protease inhibitor, seed storage, LTP family protein precursor
Os08g0131300* 3-磷酸甘油酰基转移酶 Glycerol-3-phosphate acyltransferase
qHD10.1 10 3.15-3.20 Os10g0152000* OsWAK类受体蛋白激酶 OsWAK receptor-like protein kinase
qHD10.2 10 3.61-3.71 Os10g0157200 丝裂原活化蛋白激酶15 Mitogen-activated protein kinase 15
Os10g0157400* 钙依赖性蛋白激酶12 Calcium-dependent protein kinase 12
Os10g0158400* 查尔酮合酶 Chalcone synthase

Fig. 3

Gene structure and non-synonymous mutation of candidate genes between TD70 and Kasalath A: Os07g0434700; B: Os08g0130900; C: Os08g0131100; D: Os08g0131300; E: Os10g0152000; F: Os10g0157400; G: Os10g0158400. Frames with black lines: exon; Grey boxes: protein coding sequence; Red arrow: missense mutation; Blue arrow: frameshift variant: Black arrow: indel."

Fig. 4

Effects of different Haps of candidate genes on heading date of RIL lines HapA: the SNP of candidate genes are the same as TD70; HapB: the SNP of candidate genes are the same as Kasalath."

Table 4

Overlap of known QTLs and genes contributed to heading date with QTLs detected in this study"

QTL 本研究This study 已发表的相关位点/基因 Known QTLs or genes
染色体Chr. 物理位置
Position (Mb)
Populations or known gene
Position (Mb)
qHD3 3 21.75-21.81 Caiapo/O. rufipogon BC2F2 19.41-22.34 29
qHD6.1 6 1.80-1.85 Nipponbare/Kasalath BC3F2 NIL 1.64-3.08 30
qHD6.2 6 10.93-11.07 Nipponbare/Kasalath BC3F2 NIL 6.82-11.68 30
V20A/IRGC 105491 BC 2 10.05-27.25 31
qHD7.1 7 14.50-14.54 Zhenshan 97/Ming 63 F2:3 7.23-16.87 32
qHD7.3 7 4.47-4.52 IR64/Azucena DH 4.57-6.78 33
Sasanishiki/Habataki BCIL 4.57-9.10 34
qHD7.4 7 28.35-28.37 IR64/Azucena DH 28.41-29.46 30
Gui630/Taiwanjing DH 27.78-29.26 35
OsCOL13 28.18 16, 36
qHD12 12 26.21-26.27 IR64/Azucena DH 24.85-27.49 30
Lemont/Teqing RIL 26.11-26.99 37, 38
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