QTL mapping and analysis candidate genes for heading stage in Echinochloa based on bulked segregant analysis

doi:10.11686/cyxb2025117

Abstract

Abstract:

Heading date is a crucial agronomic trait that significantly influences crop yield formation and environmental adaptability. Elucidating the molecular regulatory mechanisms of heading date is essential for forage germplasm innovation and for breeding new varieties. Echinochloa species （barnyard grass） are ideal forage resources for marginal land utilization because of their remarkable salt-alkali tolerance. However， the molecular mechanisms underlying the regulation of heading date in Echinochloa remain unclear. This knowledge gap substantially constrains molecular breeding of ecologically adapted varieties and the agricultural development of areas with saline-alkali soils. To decipher the genetic regulatory network controlling heading date in barnyard grass， we employed bulked segregant analysis sequencing （BSA-Seq） to analyze Echinochloa crusgalli var. frumentacea， Echinochloa crusgalli var. mitis， and their F_2∶3 hybrid population （62 samples in total）， using the Echinochloa genome as a reference. Then， quantitative trait locus （QTL） mapping was performed using the Index algorithm in R 4.2.2， and a protein-protein interaction network was constructed using the String database to identify candidate genes. Functional annotation of these genes was conducted using the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases. A total of 11347 single nucleotide polymorphisms and 1992 insertion/deletion mutations were identified as effective variants. Two candidate QTLs were mapped： qHD-16-1 （193.14 kb， containing 17 genes） and qHD-6-1 （11.05 kb， containing two genes）. Six key candidate genes ［EcRCS3， EcCYSK （missense mutation）， EcP0710H01.9， EcAPG， EcCFAT， and EcNBA1］ were identified. Functional annotation revealed that these genes regulate heading date primarily by modulating sulfur， cysteine， and methionine metabolic pathways， thereby influencing the expression of flowering-related genes and flower bud differentiation. This study provides valuable genetic resources and potential molecular targets for molecular marker-assisted breeding and offers critical insights into the molecular mechanisms underlying the regulation of heading date in barnyard grass （Echinochloa spp.）. These findings establish a theoretical foundation for precision breeding of saline-alkali-adapted forage varieties， demonstrating significant scientific merit and promising application prospects for the utilization of saline-alkali land.

Key words: Echinochloa, heading stage, BSA-seq, QTL mapping, candidate genes analysis

Gang ZHANG, Xing XU, Lin ZHU. QTL mapping and analysis candidate genes for heading stage in Echinochloa based on bulked segregant analysis[J]. Acta Prataculturae Sinica, 2026, 35(3): 210-222.

Figures/Tables 12

References 40

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样本名 Sample ID	宁夏无芒稗 E. crusgalli var. mitis	湖南稷子 E. crusgalli var.frumentacea	早抽穗混合池 Early heading pool	晚抽穗混合池 Late heading pool
原始序列数Raw reads	110698444	97387918	293041906	296602604
原始碱基数Raw bases （bp）	16715465044	14705575618	44249327806	44786993204
过滤序列数Clean reads	108936494	95849704	287622304	291064822
过滤碱基数Clean bases （bp）	16249584281	14308880560	42973291907	43460506570
GC含量GC content （%）	48.35	46.63	45.73	46.13
Q₃₀含量Q₃₀ content （%）	94.82	94.96	94.97	95.06
比对率Mapped ratio （%）	99.72	99.75	98.97	99.48
优质比对率Proper ratio （%）	96.38	96.61	96.07	96.60
插入片段长度Insert fregment length （bp）	338	345	323	310
平均测序深度Average sequencing depth	13.20	11.58	33.81	34.42
覆盖度（≥1×） Coverage （≥1×）（%）	91.57	91.93	93.84	93.69
覆盖度（≥4×） Coverage （≥4×）（%）	81.55	84.93	91.36	91.35

样本名 Sample ID	宁夏无芒稗 E. crusgalli var. mitis	湖南稷子 E. crusgalli var.frumentacea	早抽穗混合池 Early heading pool	晚抽穗混合池 Late heading pool
原始序列数Raw reads	110698444	97387918	293041906	296602604
原始碱基数Raw bases （bp）	16715465044	14705575618	44249327806	44786993204
过滤序列数Clean reads	108936494	95849704	287622304	291064822
过滤碱基数Clean bases （bp）	16249584281	14308880560	42973291907	43460506570
GC含量GC content （%）	48.35	46.63	45.73	46.13
Q₃₀含量Q₃₀ content （%）	94.82	94.96	94.97	95.06
比对率Mapped ratio （%）	99.72	99.75	98.97	99.48
优质比对率Proper ratio （%）	96.38	96.61	96.07	96.60
插入片段长度Insert fregment length （bp）	338	345	323	310
平均测序深度Average sequencing depth	13.20	11.58	33.81	34.42
覆盖度（≥1×） Coverage （≥1×）（%）	91.57	91.93	93.84	93.69
覆盖度（≥4×） Coverage （≥4×）（%）	81.55	84.93	91.36	91.35

SNP变异位点信息 SNP variation sites information	宁夏无芒稗 E. crusgalli var. mitis	湖南稷子 E. crusgalli var.frumentacea	早抽穗混合池Early heading pool	晚抽穗混合池Late heading pool	Indel变异位点信息 Indel variation sites information	宁夏无芒稗 E. crusgalli var. mitis	湖南稷子 E. crusgalli var.frumentacea	早抽穗混合池Early heading pool	晚抽穗混合池 Late heading pool
起始密码子丢失Start lost	538	521	550	557	起始密码子丢失Start lost	176	177	198	188
终止密码子丢失Stop lost	539	536	586	553	终止密码子丢失Stop lost	167	165	184	188
终止密码子获得Stop gained	2874	2934	3252	3030	终止密码子获得Stop gained	454	452	528	509
非同义突变Nonsynonymous mutation	118535	120467	129985	124244	基因区间Intragenic region	411710	418151	469267	448800
同义突变Synonymous mutation	67254	68338	73371	70561	移码突变Frameshift mutation	16809	16500	18908	18208
基因区间Intragenic region	2420168	2436130	2621923	2544620	非编码转录突变Non coding transcript mutation	15	12	13	17
终止子编码突变Stop retained mutation	104	111	118	113	外显子缺失突变Exon loss mutation	5	4	6	3
SNP和Sum SNP	2610012	2629037	2829785	2743678	Indel和Sum Indel	429336	435461	489104	467913
SNP总数Total SNP	2882936	2919872	3139343	3039142	Indel总数Total Indel	511925	523408	582001	558165

SNP变异位点信息 SNP variation sites information	宁夏无芒稗 E. crusgalli var. mitis	湖南稷子 E. crusgalli var.frumentacea	早抽穗混合池Early heading pool	晚抽穗混合池Late heading pool	Indel变异位点信息 Indel variation sites information	宁夏无芒稗 E. crusgalli var. mitis	湖南稷子 E. crusgalli var.frumentacea	早抽穗混合池Early heading pool	晚抽穗混合池 Late heading pool
起始密码子丢失Start lost	538	521	550	557	起始密码子丢失Start lost	176	177	198	188
终止密码子丢失Stop lost	539	536	586	553	终止密码子丢失Stop lost	167	165	184	188
终止密码子获得Stop gained	2874	2934	3252	3030	终止密码子获得Stop gained	454	452	528	509
非同义突变Nonsynonymous mutation	118535	120467	129985	124244	基因区间Intragenic region	411710	418151	469267	448800
同义突变Synonymous mutation	67254	68338	73371	70561	移码突变Frameshift mutation	16809	16500	18908	18208
基因区间Intragenic region	2420168	2436130	2621923	2544620	非编码转录突变Non coding transcript mutation	15	12	13	17
终止子编码突变Stop retained mutation	104	111	118	113	外显子缺失突变Exon loss mutation	5	4	6	3
SNP和Sum SNP	2610012	2629037	2829785	2743678	Indel和Sum Indel	429336	435461	489104	467913
SNP总数Total SNP	2882936	2919872	3139343	3039142	Indel总数Total Indel	511925	523408	582001	558165

Loess拟合Loess fitting			滑窗策略Sliding window strategy
染色体Chromosome	开始位置Start position	结束位置End position	染色体Chromosome	开始位置Start position	结束位置End position
2	17062211	51531094	1	4108439	9491129
6	6601800	16813256	13	9003411	9044483
7	6840956	9180095	14	40414541	49041093
21	10182932	41322793	16	1612839	2819921
24	28707547	28722744	17	32032451	32989414
26	15686452	36334572	26	15686452	36334572
4	5777936	5787128	6	16802203	16813256
			7	3110078	8649515
			8	19854393	24310847
			2	17062211	51531094
			4	5777936	5787128