利用BSA-seq技术挖掘油菜耐铝毒基因

doi:10.7668/hbnxb.20196292

摘要/Abstract

摘要：

近年来,我国南方地区农田土壤酸化现象日益严重,导致土壤中铝离子活性增强,对作物生长产生明显毒害作用,为挖掘油菜耐铝毒相关性状基因位点,以耐铝毒品种R248与铝毒敏感品种S120杂交得到的F₂群体为试验材料,通过表型鉴定构建铝毒耐受性极端混池,并采用BSA-seq法进行QTL定位分析。表型鉴定结果表明,F₂群体的铝毒耐受性呈连续性正态分布;通过基因组测序、变异位点筛选及性状关联研究,在A07、C02、C03和C08 4条染色体上鉴定出4个显著影响铝毒耐受性的遗传区域,区间总长度为0.73 Mb,含98个基因;根据富集分析结果和基因注释信息,预测BnaA07g35600D、BnaA07g35660D、BnaA07g35700D、BnaA07g35710D和BnaC03g39670D参与油菜耐铝毒激素的合成与运输;BnaC03g39840D参与细胞壁果胶甲酯酶合成;BnaC03g39750D和BnaC08g20580D为含MYB结构的转录因子;BnaC03g39850D和BnaC03g39980D参与氨基酸代谢,这些基因与油菜铝毒耐受性的相关性较大,为后续开展耐铝毒相关基因的分离鉴定及其分子机制解析提供了重要依据。

关键词: 油菜, 铝毒, BSA-seq, 候选基因

Abstract:

In recent years,soil acidification and aluminum ion toxicity in southern cultivated land have intensified.To explore the gene loci related to aluminum tolerance in rapeseed,the F₂ population obtained by crossing the aluminum tolerant variety R248 with the aluminum sensitive variety S120 was used as the experimental material.The extreme mixed pool of aluminum toxicity tolerance was constructed by phenotypic identification,and QTL localization analysis was performed by BSA-seq.The phenotype identification results showed that the aluminum toxicity tolerance of the F₂ population exhibited a continuous normal distribution.After sequencing,mutation detection,and association analysis,a total of 4 intervals related to aluminum toxicity tolerance were obtained,distributed on chromosomes A07,C02,C03,and C08,with a total length of 0.73 Mb and 98 genes.Based on the enrichment analysis results and gene annotation information,it is predicted that BnaA07g35600D,BnaA07g35660D,BnaA07g35700D,BnaA07g3570D, and BnaC03g39670D will participate in the synthesis and transportation of aluminum tolerance hormones in rapeseed,BnaC03g39840D participates in the synthesis of cell wall pectinesterase,BnaC03g39750D and BnaC08g20580D were transcription factors with MYB structure,BnaC03g39850D and BnaC03g39980D were involved in amino acid metabolism.These genes are highly correlated with aluminum tolerance in rapeseed,laying the foundation for the cloning and functional research of aluminum tolerance genes in the next step.

Key words: Brassica napus L., Aluminum toxicit, BSA-seq, Candidate gene

中图分类号:

S565.4

张美薇, 陈明, 韩德鹏, 李亚贞, 肖小军, 熊文, 黄天宝, 程业伟, 张晨, 周莺, 郑伟. 利用BSA-seq技术挖掘油菜耐铝毒基因[J]. 华北农学报, 2026, 41(1): 30-38. doi: 10.7668/hbnxb.20196292.

ZHANG Meiwei, CHEN Ming, HAN Depeng, LI Yazhen, XIAO Xiaojun, XIONG Wen, HUANG Tianbao, CHENG Yewei, ZHANG Chen, ZHOU Ying, ZHENG Wei. Exploring Aluminum Tolerance Genes in Brassica napus Based on BSA-seq[J]. Acta Agriculturae Boreali-Sinica, 2026, 41(1): 30-38. doi: 10.7668/hbnxb.20196292.

http://www.hbnxb.net/CN/Y2026/V41/I1/30

图/表 9

图1 F₂表型鉴定 R248.耐铝父本;S120.铝敏感母本;CK.对照;T.150 μmol/L AlCl₃处理。

Fig.1 F₂ phenotypic identification R248.Aluminum-tolerant male parent;S120.Aluminum-sensitive female parent;CK.Control;T.150 μmol/L AlCl₃ treatment.

表1 BSA-seq测序数据统计

Tab.1 Statistics of BSA-seq sequenced reads

样品 Sample	原始碱基数/bp Raw bases	高质量碱基数/bp Clean bases	Q20/%	Q30/%	GC 含量/% GC content
R248	11 865 770 100	11 608 838 100	98.66	96.34	37.59
S120	11 221 807 800	10 997 508 300	98.73	96.55	37.41
BnaRF2	37 068 239 100	36 162 695 100	97.31	92.86	37.65
BnaSF2	30 531 714 600	29 793 675 300	98.11	94.72	37.70

表2 比对结果统计

Tab.2 Comparison result statistics

样品 Sample	总reads数 Total reads	比对reads数 Mapped reads	比对率/% Mapping rate	深度/× Depth	覆盖度/% Coverage
R248	77 392 254	76 463 182	98.80	12.98	92.36
S120	73 316 722	72 259 034	98.56	12.20	91.09
BnaRF2	241 084 634	237 490 700	98.51	37.33	96.70
BnaSF2	198 624 502	195 864 711	98.61	34.36	96.49

表3 SNP注释统计

Tab.3 SNP annotation statistics个

类别 Category	父本 R248	母本 S120	耐铝混池 BnaRF2	铝敏感混池 BnaSF2
外显子 Exonic	475 614	568 540	845 322	842 275
外显子终止位点获得 Exonic stop gain	2 758	3 305	4 876	4 878
外显子终止位点缺失 Exonic stop loss	670	789	1 201	1 190
外显子同义突变 Exonic synonymous	277 106	331 708	493 820	491 814
外显子非同义突变 Exonic non-synonymous	195 080	232 738	345 425	344 393
内含子 Intronic	437 756	518 381	786 483	781 894
剪接 Splicing	1 880	2 359	3 369	3 340
上游 Upstream	307 434	367 416	545 231	544 291
下游 Downstream	254 490	303 816	453 128	451 073
上游/下游 Upstream/Downstream	63 705	76 221	113 439	113 706
基因间区 Intergenic	1 896 598	2 170 181	3 252 827	3 235 603
3'非翻译区 3'UTR	45 513	55 364	81 530	81 325
5'非翻译区 5'UTR	30 910	36 788	54 621	54 545
总计 Total	3 513 900	4 099 066	6 135 950	6 108 052

表4 InDel注释统计

Tab.4 InDel annotation statistics个

类别 Category	父本 R248	母本 S120	耐铝混池 BnaRF2	铝敏感混池 BnaSF2
外显子 Exonic	27 999	33 002	50 177	50 084
外显子终止位点获得 Exonic stop gain	749	914	1 502	1 487
外显子终止位点缺失 Exonic stop loss	90	111	164	167
外显子移码删除 Exonic frameshift deletion	8 522	9 952	14 943	14 952
外显子移码插入 Exonic frameshift insertion	7 389	8 454	13 059	12 915
外显子非移码删除 Exonic non-frameshift deletion	5 977	7 186	10 751	10 739
外显子非移码插入 Exonic non-frameshift insertion	5 272	6 385	9 758	9 824
上游 Upstream	98 816	116 536	179 828	179 153
内含子 Intronic	171 505	201 167	313 889	312 086
剪接 Splicing	1 729	2 075	3 187	3 159
下游 Downstream	73 686	87 182	134 295	134 120
上游/下游 Upstream/Downstream	25 608	29 775	46 246	46 261
基因间区 Intergenic	297 998	346 380	531 746	529 830
3'非翻译区 3'UTR	20 092	23 799	36 123	36 038
5'非翻译区 5'UTR	16 055	18 768	28 421	28 464
总计 Total	733 184	858 334	1 323 493	1 318 780

图2 子代 All-index 在染色体上的分布

Fig.2 Distribution of progeny All-index on chromosomes

图3 2个子代Δ(All-index)在染色体上的分布

Fig.3 Distribution of Δ(All-index)from the two progeny on the chromosome

图4 候选区域内基因的通路分布 A.GO富集分析图:生物学过程1.通过细胞板形成完成细胞分裂,2.细胞分裂过程,3.有丝分裂细胞分裂过程,4.有丝分裂细胞质分裂,5.依赖细胞骨架的细胞分裂,6.分裂期细胞内囊泡运输,7.气孔复合体发育,8.有丝分裂细胞周期的调控,9.rDNA的维护,10.末端复制负向调节,11.DNA重复元件的维护,12.通过同源重组调节双链断裂修复,13.末端复制调控,14.双链断裂修复的调控,15.DNA重组的负向调控,16.DNA重组的调控,17.DNA修复的调控,18.染色体组织的负向调控,19.DNA代谢过程的负向调控,20.对DNA损伤刺激响应的过时调控机制,21.保护母细胞胞质分裂,22.有丝分裂细胞周期的G1/S期转换,23.细胞组分,24.细胞周期G1/S期转换的调控,25.细胞周期G1/S期转换;细胞组分1.皮质微管,垂直于长轴,2.食管前带,3.皮质微管,4.皮质微管细胞骨架,5.细胞质微管,6.皮质细胞骨架,7.细胞周期蛋白依赖性蛋白激酶全酶复合物,8.丝氨酸/苏氨酸蛋白激酶复合物,9.蛋白激酶复合物,10.NatA复合体;分子功能1.结合DNA聚合酶,2.结合细胞周期蛋白,3.细胞周期蛋白依赖性丝氨酸/苏氨酸激酶活性,4.细胞周期依赖性蛋白激酶活性,5.蔗糖跨膜转运蛋白活性,6.双糖跨膜转运蛋白活性,7.寡糖跨膜转运蛋白活性,8.赤霉素3-β-双加氧酶活性。B.KEGG通路分析图:1.硫胺素代谢,2.甘油磷脂代谢,3.磷脂酰肌醇信号系统,4.非同源末端连接,5.甘油酯质代谢,6.昼夜节律-植物,7.嘌呤代谢,8.乙醛酸盐和二羧酸盐代谢,9.甘氨酸、丝氨酸和苏氨酸代谢,10.二萜生物合成,11.赖氨酸降解,12.糖酵解/葡萄糖生成,13.缬氨酸、亮氨酸和异亮氨酸降解,14.丙酮酸代谢,15.色氨酸代谢,16.柠檬酸循环(TCA循环),17.丙酸代谢,18.各种植物次生代谢物的生物合成,19.半胱氨酸和蛋氨酸代谢。

Fig.4 Distribution of gene pathways within candidate regions A.GO enrichment analysis:Biological process 1.Cytokinesis by cell plate formation,2.Cytokinetic process,3.Mitotic cytokinetic process,4.Mitotic cytokinesis,5.Cytoskeleton-dependent cytokinesis,6.Cytokinesis vacuolar transport,7.Stomatal complex development,8.Regulation of mitotic cell cycle,9.Maintenance of rDNA,10.Negative regulation of telomere maintenance,11.Maintenance of DNA repeat elements,12.Regulation of double-strand break repair via homologous recombination,13.Regulation of telomere maintenance,14.Regulation of double-strand break repair,15.Negative regulation of DNA recombination,16.Regulation of DNA recombination,17.Regulation of DNA repair,18.Negative regulation of chromosome organization,19.Negative regulation of DNA metabolic process,20.Obsolete regulation of response to DNA damage stimulus,21.Guard mother cell cytokinesis,22.G1/S transition of mitotic cell cycle,23.Cellular component,24.Regulation of cell cycle G1/S phase transition,25.Cell cycle G1/S phase transition;Cellular component 1.Cortical microtubule,transverse to long axis,2.Preprophase band,3.Cortical microtubule,4.Cortical microtubule cytoskeleton,5.Cytoplasmic microtubule,6.Cortical cytoskeleton,7.Cyclin-dependent protein kinase holoenzyme complex,8.Serine/threonine protein kinase complex,9.Protein kinase complex,10.NatA complex;Molecular function 1.DNA polymerase binding,2.Cyclin binding.3.Cyclin-dependent protein serine/threonine kinase activity,4.Cyclin-dependent protein kinase activity,5.Sucrose transmembrane transporter activity,6.Disaccharide transmembrane transporter activity,7.Oligosaccharide transmembrane transporter activity,8.Gibberellin 3-beta-dioxygenase activity.B.KEGG pathway analysis:1.Thiamine metabolism,2.Glycerophospholipid metabolism,3.Phosphatidylinositol signaling system,4.Non-homologous end-joining,5.Glycerolipid metabolism,6.Circadian rhythm-plant,7.Purine metabolism,8.Glyoxylate and dicarboxylate metabolism,9.Glycine,serine and threonine metabolism,10.Diterpenoid biosynthesis,11.Lysine degradation,12.Glycolysis/Gluconeogenesis,13.Valine,leucine and isoleucine degradation,14.Pyruvate metabolism,15.Tryptophan metabolism,16.Citrate cycle (TCA cycle),17.Propanoate metabolism,18.Biosynthesis of various plant secondary metabolites,19.Cysteine and methionine metabolism.

表5 候选基因及功能注释

Tab.5 Candidate genes and functional annotations

基因ID Gene ID	拟南芥同源基因 Arabidopsis homologous genes	基因功能注释 Function annotation
BnaA07g35600D	AT1G15690	AVP1
BnaA07g35660D	AT1G80390	吲哚乙酸诱导蛋白15
BnaA07g35700D	AT1G80340	赤霉素3;氧化酶2
BnaA07g35710D	AT1G80340	赤霉素3;氧化酶2
BnaC03g39670D	AT3G16500	光敏色素相关蛋白1
BnaC03g39750D	AT3G16857	反应调节剂1
BnaC03g39840D	AT3G17060	果胶裂解酶样超家族蛋白
BnaC03g39850D	AT3G17090	蛋白磷酸酶2C家族蛋白
BnaC03g39980D	AT3G17410	蛋白激酶超家族蛋白
BnaC08g20580D	AT3G48920	MYB结构域蛋白45

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