基于BSA-seq发掘水稻抽穗期相关QTLs及候选基因

doi:10.13304/j.nykjdb.2024.0216

摘要/Abstract

摘要：

抽穗期作为水稻重要的性状之一，不仅与水稻生育时期密切相关，还与水稻产量、品质和抗逆性密切相关，决定了水稻品种的种植地区和季节适应性，因此，定位水稻抽穗期相关基因在水稻生产中有着重要的作用。利用HQ20和金23B及其杂交构建的F₄群体为试验材料，根据群体中水稻抽穗期划分3个等级：抽穗期早、抽穗期适中、大青棵（不抽穗），并构建早、中、青3个混池，采用BSA-seq（bulked-segregant analysis sequencing）方法挖掘水稻抽穗期基因。结果表明，BSA-seq结果与参考基因组比对率在94%以上，4×基因组覆盖率在80%以上；基于此，在置信度为0.95时，经SNP-index算法获得位于4条染色体（6、7、8和9号）的17个SNPs与Indels一致的关联区间，进一步分析区域内的候选基因，发现61个基因存在非同义突变。GO与KEGG富集分析表明，与水稻抽穗期密切相关的途径有UDP-糖基转移酶活性、细胞周期G2/M期转变的正向调控和植物激素信号转导等。结合3K水稻数据库中的单倍型分析与已公布的表达量数据，挖掘出3个抽穗期关键候选基因：LOC_Os07g22720、LOC_Os07g23740、LOC_Os08g07200。以上结果为开展水稻抽穗期性状遗传改良以及遗传基础解析奠定了基础。

关键词: 水稻, 抽穗期, BSA-seq, 候选基因

Abstract:

As one of the important traits of rice， rice heading date is closely related not only to the rice growth period but also to rice yield， quality and stress resistance， which determines the planting area and seasonal adaptability of rice varieties. Therefore， the location of rice heading date related genes plays an important role in rice production. In this study， HQ20， Jin 23B and their F₄ population constructed were used as the materials. According to the heading stage of the rice in the population， it was divided into 3 levels including early， middle and green plant （not heading）， and 3 mixed pools of early， middle and green were constructed. The bulked-segregant analysis sequencing （BSA-seq） method was used to discover rice heading period genes. The results showed that the comparison rate between BSA-seq results and the reference genome was over 94%， and the 4× genome coverage rate was over 80%. Based on this， when the confidence level was 0.95， by SNP-index algorithm 17 SNPs located on 4 chromosomes （6， 7， 8 and 9） were obtained which had consistent association intervals with indel. Further analysis of candidate genes in the region found that 61 genes had non-synonymous mutations. GO and KEGG enrichment analysis showed that pathways closely related to rice heading stage included UDP-glycosyltransferase activity， positive regulation of cell cycle G2/M phase transition， and phytohormone signal transduction. Finally， combining haplotype analysis in the 3K rice database and published expression data， 3 key candidate genes for heading stage were discovered including LOC_Os07g22720， LOC_Os07g23740 and LOC_Os08g07200. The above results laid the foundation for genetic improvement of rice heading period traits and analysis of genetic basis.

Key words: rice, heading date, BSA-seq, candidate genes

中图分类号:

S511

魏荣华, 尹明, 王文生, 崔彦茹. 基于BSA-seq发掘水稻抽穗期相关QTLs及候选基因[J]. 中国农业科技导报, 2024, 26(9): 12-24.

Ronghua WEI, Ming YIN, Wensheng WANG, Yanru CUI. Discovering of QTLs and Candidate Genes Related to Rice Heading Period Traits Based on BSA-seq[J]. Journal of Agricultural Science and Technology, 2024, 26(9): 12-24.

图/表 14

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样品 Sample	过滤后数据 Clean data/bp	Q30/%	GC/%	总读段 Total reads	读段比对率 Mapped reads/%	覆盖度 Coverage rate/%
样品 Sample	过滤后数据 Clean data/bp	Q30/%	GC/%	总读段 Total reads	读段比对率 Mapped reads/%	1×	4×
HQ31	5 744 148 300	92.02	41.25	35 621 290	96.69	89.98	81.90
OHQ20	5 343 193 500	91.24	42.09	38 294 322	96.87	90.43	82.90
适中Moderate	19 863 114 000	91.69	44.01	12 1353 842	96.86	95.22	92.36
青棵Green	18 203 076 300	91.94	45.05	132 420 760	96.70	95.83	92.77
早熟Early	19 540 310 100	91.57	44.81	130 268 734	94.75	96.09	92.93

样品 Sample	过滤后数据 Clean data/bp	Q30/%	GC/%	总读段 Total reads	读段比对率 Mapped reads/%	覆盖度 Coverage rate/%
样品 Sample	过滤后数据 Clean data/bp	Q30/%	GC/%	总读段 Total reads	读段比对率 Mapped reads/%	1×	4×
HQ31	5 744 148 300	92.02	41.25	35 621 290	96.69	89.98	81.90
OHQ20	5 343 193 500	91.24	42.09	38 294 322	96.87	90.43	82.90
适中Moderate	19 863 114 000	91.69	44.01	12 1353 842	96.86	95.22	92.36
青棵Green	18 203 076 300	91.94	45.05	132 420 760	96.70	95.83	92.77
早熟Early	19 540 310 100	91.57	44.81	130 268 734	94.75	96.09	92.93

染色体 Chromosome	起始位置 Start position/bp	终止位置 End position/bp	基因数量 Gene number
Chr5	9 171 001	9 172 000	1
Chr5	15 980 001	15 981 000	1
Chr6	819 788	862 809	2
Chr6	24 267 001	24 268 000	1
Chr7	3 282 221	3 515 234	5
Chr7	7 078 687	7 184 099	6
Chr7	7 661 654	8 210 957	19
Chr7	9 362 884	13 851 724	151
Chr7	14 502 162	16 910 700	57
Chr7	17 474 000	17 474 209	1
Chr7	26 393 554	26 913 290	5
Chr7	28 410 165	28 428 916	3
Chr8	559 292	634 638	3
Chr8	1 038 578	1 075 302	5
Chr8	3 660 741	4 179 420	13
Chr8	5 032 940	5 032 946	1
Chr8	6 217 190	6 217 199	1
Chr8	9 001 410	9 001 425	1
Chr8	9 310 563	9 510 022	2
Chr8	10 365 320	10 920 326	6
Chr8	11 279 434	11 279 468	1
Chr8	11 589 580	11 589 588	1
Chr8	12 272 300	12 272 330	1
Chr8	13 063 007	13106 062	2
Chr8	13 692 000	13 692 049	1
Chr8	14 083 249	14 330 070	4
Chr8	14 732 433	14 913 038	2
Chr8	15 216 765	15 796 339	6
Chr8	16 630 600	16 630 619	1
Chr8	17 148 084	17 153 579	2
Chr8	18 006 500	18 006 529	1
Chr8	18 345 182	18 452 701	2
Chr8	18 803 600	18 803 609	1
Chr8	19 730 003	20 312 233	16
Chr9	19 462 800	19 462 880	1
Chr9	20 098 700	20 098 749	1
Chr10	260 200	260 233	1
Chr11	6 523 296	6 613 238	3
Chr11	19 092 100	19 092 108	1
Chr12	3 918 600	3 918 631	1
Chr12	10 337 833	10 337 834	1

染色体 Chromosome	起始位置 Start position/bp	终止位置 End position/bp	基因数量 Gene number
Chr5	9 171 001	9 172 000	1
Chr5	15 980 001	15 981 000	1
Chr6	819 788	862 809	2
Chr6	24 267 001	24 268 000	1
Chr7	3 282 221	3 515 234	5
Chr7	7 078 687	7 184 099	6
Chr7	7 661 654	8 210 957	19
Chr7	9 362 884	13 851 724	151
Chr7	14 502 162	16 910 700	57
Chr7	17 474 000	17 474 209	1
Chr7	26 393 554	26 913 290	5
Chr7	28 410 165	28 428 916	3
Chr8	559 292	634 638	3
Chr8	1 038 578	1 075 302	5
Chr8	3 660 741	4 179 420	13
Chr8	5 032 940	5 032 946	1
Chr8	6 217 190	6 217 199	1
Chr8	9 001 410	9 001 425	1
Chr8	9 310 563	9 510 022	2
Chr8	10 365 320	10 920 326	6
Chr8	11 279 434	11 279 468	1
Chr8	11 589 580	11 589 588	1
Chr8	12 272 300	12 272 330	1
Chr8	13 063 007	13106 062	2
Chr8	13 692 000	13 692 049	1
Chr8	14 083 249	14 330 070	4
Chr8	14 732 433	14 913 038	2
Chr8	15 216 765	15 796 339	6
Chr8	16 630 600	16 630 619	1
Chr8	17 148 084	17 153 579	2
Chr8	18 006 500	18 006 529	1
Chr8	18 345 182	18 452 701	2
Chr8	18 803 600	18 803 609	1
Chr8	19 730 003	20 312 233	16
Chr9	19 462 800	19 462 880	1
Chr9	20 098 700	20 098 749	1
Chr10	260 200	260 233	1
Chr11	6 523 296	6 613 238	3
Chr11	19 092 100	19 092 108	1
Chr12	3 918 600	3 918 631	1
Chr12	10 337 833	10 337 834	1

染色体 Chromosome	起始位置 Start position/bp	终止位置 End position/bp	基因数量 Gene number
Chr5	7 966 753	8 080 035	2
Chr6	867 000	867 072	2
Chr6	24 267 600	24 267 692	1
Chr7	5 651 500	5 651 596	1
Chr7	7 145 117	7 206 410	3
Chr7	7 928 606	8 179 003	5
Chr7	9 564 466	10 124 576	4
Chr7	10 499 474	11 646 584	12
Chr7	12 529 769	13 851 742	29
Chr7	14 503 097	15 243 927	10
Chr7	15 876 095	16 832 885	12
Chr7	17 399 500	17 399 542	1
Chr8	559 300	559 352	1
Chr8	1 040 057	1 050 460	3
Chr8	3 948 972	4 283 090	4
Chr8	5 623 000	5 623 045	1
Chr8	10 447 300	10 447 314	1
Chr8	14 970 700	14 970 730	1
Chr8	15 598 900	15 598 941	1
Chr8	18 006 500	18 006 549	1
Chr8	18 452 681	18 452 693	1
Chr8	19 739 048	20 197 724	11
Chr9	19 759 500	19 759 596	2
Chr9	20 098 700	20 098 775	1
Chr11	5 919 041	6 002 538	2
Chr11	18 350 200	18 350 292	1
Chr12	10 137 200	10 137 217	1