青稞早抽穗主效QTL cqHD2H-2的遗传定位及候选基因分析

doi:10.3724/SP.J.1006.2022.11071

Abstract

Abstract:

Heading date is closely linked with agronomic performance, which is responsible for the regional and seasonal adaptation of barley varieties, and it is also a key indicator of the early or later maturity in barley. Previous studies indicated that the major QTL cqHD2H-2 for early heading was located in an 84 Mb interval on chromosome 2H of barley. To further verify the effective stability of the cqHD2H-2, in this study, we validated this locus and analyzed candidate genes. New InDel markers were developed based on the primary mapping region of cqHD2H-2 through an F₅ population constructed from the cross of DZZ (early heading) and KL10 (late heading). A total of three markers tightly linked to the target gene were obtained, and one flank marker was confirmed as co-dominant marker by scanning 25 extreme early heading and 25 extreme late heading individuals of F₅ population, which mapped the locus cqHD2H-2 located in a 40 Mb region between PA22 and Va07 on the chromosome 2H. The homologous gene HORVU2Hr1G087460 (HvNF-YB3) of rice heading date gene DTH8 in barley was acquired by homologous collinearity comparison of the region between barley and rice. Compared with the full length of HvNF-YB3 gene, the encoding region of Hv2H.NF-YB3 (DZZ) and Hv2H.nf-yb3 (KL10) was composed of an exon. The encoding region was 750 bp, and the promoter region was 2116 bp. There were three SNPs detected between the promoter region of Hv2H.NF-YB3 and Hv2H.nf-yb3. The relative expression levels of Hv2H.NF-YB3 and Hv2H.nf-yb3 showed that there were significant differences in the transcriptional level. Hv2H.NF-YB3 and Hv2H.nf-yb3 expressed in stem, awn, and glume, compared with Hv2H.NF-YB3, the relative expression levels of Hv2H.nf-yb3 significantly decreased in the three tissues. The relative expression levels gradually decreased with the development of the plants. In conclusion, Hv2H.NF-YB3 may play a role in the regulation of heading time in barley. The results were useful for developing early heading lines by marker-assisted selection (MAS) and laid a foundation for fine mapping and subsequent map-based cloning of cqHD2H-2.

Key words: barley, cqHD2H-2, molecular marker, genetic map, HvNF-YB3

YU Xin-Lian, LI Xin, YAO Xiao-Hua, YAO You-Hua, BAI Yi-Xiong, AN Li-Kun, WU Kun-Lun. Genetic mapping and candidate gene analysis of the major QTL cqHD2H-2 for early heading in barley (Hordeum vulgare L.)[J].Acta Agronomica Sinica, 2022, 48(10): 2463-2474.

Figures/Tables 8

Table 1

Fig. 1

Table 2

Fig. 2

Fig. 3

Fig. 4

Table 3

Structure of elements in promoter region of Hv2H.NF-YB3"

顺式作用元件 Cis-acting element	核心序列 Core motif	数量 Number	位置 Position	功能 Function
AT-rich element	ATAGAAATCAA	1	+204	富含AT的DNA结合蛋白(ATBP-1)结合位点 Binding site of AT-rich DNA binding protein (ATBP-1)
A-box	CCGTCC	3	-1212/+1991/+1976	顺式调控元件 Cis-acting regulatory element
ABRE	ACGTG/TACGGTC/ GCAACGTGTC	5	+699/+1851/+1013/ -901/+1848	参与脱落酸响应的顺式作用元件 Cis-acting element involved in the abscisic acid responsiveness
ARE	AAACCA	1	+50	厌氧诱导必需顺式调节元件 Cis-acting regulatory element essential for the anaerobic induction
ATC-motif	AGTAATCT/ AATCTAATCC	1	-1405	参与光响应的部分保守DNA模块 Part of a conserved DNA module involved in light responsiveness
ATCT-motif	AATCTAATCC	1	+1362	参与光响应的部分保守DNA模块 Part of a conserved DNA module involved in light responsiveness
AuxRR-core	GGTCCAT	2	-280/+1016	参与生长素响应的顺式调控元件 Cis-acting regulatory element involved in auxin responsiveness
Box 4	ATTAAT	1	+763	参与光响应的部分保守DNA模块 Part of a conserved DNA module involved in light responsiveness
CAAT-box	CCAAT/CAAT	29	+35/-471/+916/+1066/ +1154/-1156/-1428/ -1628, etc.	启动子和增强子区的共顺式作用元件 Common cis-acting element in promoter and enhancer regions
CCAAT-box	CAACGG	1	+814	MYBHv1结合位点 MYBHv1 binding site
CGTCA-motif	CGTCA	2	+750/+910	参与茉莉酸甲酯响应的顺式调控元件 Cis-acting regulatory element involved in the MeJA-responsiveness
circadian	CAAAGATATC	1	+79	参与昼夜节律控制的顺式调节元件 Cis-acting regulatory element involved in circadian control
GATA-motif	GATAGGG/ AAGGATAAGG	2	-981/-1364	部分光响应元件 Part of a light responsive element
G-box	TAACACGTAG/ CACGTT/CACGAC	4	-1319/-1849/-698/ -1850	参与光响应的顺式调节元件 Cis-acting regulatory element involved in light responsiveness
GT1-motif	GGTTAA	1	-1161	光响应元件 Light responsive element
MRE	AACCTAA	1	+1362	参与光响应的MYB结合位点 MYB binding site involved in light responsiveness
O2-site	GATGATGTGG	2	-310/+1681	参与玉米醇溶蛋白代谢调节的顺式调控元件 Cis-acting regulatory element involved in zein metabolism regulation
TATA-box	TATA/TATAA/ TATAAAT/ATATAT/ ATATAA/TATACA/ TACAAAA	27	-680/+681/+876/ -1186/ -1313/+1470//-1614/ -1811/+1930, etc.	转录起始-30左右的核心启动子元件 Core promoter element around -30 of transcription start
TCA-element	TCAGAAGAGG/ CCATCTTTTT	2	+108/+1565	参与水杨酸响应的顺式作用元件 Cis-acting element involved in salicylic acid responsiveness
TCT-motif	TCTTAC	1	-951	部分光响应元件 Part of a light responsive element
TGACG-motif	TGACG	2	-750/-910	参与茉莉酸甲酯响应的顺式调控元件 Cis-acting regulatory element involved in the MeJA-responsiveness

Table 3

Fig. 5

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引物 Primer	正向引物 Forward primer (5′-3′)	反向引物 Reverse primer (5′-3′)	用途 Application
Hv	CGCACTCGCATCTCTCGAT	CGAGAATACTGTGCCGCCAA	gDNA sequence amplification
Hvpro	GCCTCGCTACCCCTACTATG	CTTGGAGATCTTGGCGTTCG	Promoter sequence amplification
qHv	GAGTGCGTGTCCGAGTTCAT	GTTGATGGTCTTGCGCTTCTC	Real-time PCR
18SrRNA	CGGCTACCACATCCAAGGAA	GCTGGAATTACCGCGGCT	Real-time PCR
PA22	CCTCCTCTCTCCGCTCCAAC	CGCCTCAGCTATCTTTAAGAGCA	Flanking marker
Va07	TCGTATTCTTAGAACCATTCAACTCTCA	ATTGAAAGAAAACAAGAGATAGCAGCA	Flanking marker
VA07	TGGAGATCATTGCATGGTTCACAT	ATTGAAAGAAAACAAGAGATAGCAGCA	Flanking marker

Genetic mapping and candidate gene analysis of the major QTL cqHD2H-2 for early heading in barley (Hordeum vulgare L.)

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特异性标记 Specific marker	DZZ	KL10	极端晚抽穗单株(25) Extreme late heading plant
HVKASI	AA	aa	AA	AA	AA	AA	-	aa	aa	AA	aa	AA	AA	aa	AA	-	AA	-	-	aa	aa	AA	AA	AA	AA	AA	aa
HVKASI	AA	aa	AA	-	aa	aa	AA	aa	aa	aa	aa	aa	AA	aa	-	aa	aa	AA	aa	aa	AA	AA	AA	AA	AA	AA	AA
PA20	AA	aa	AA	AA	AA	AA	AA	AA	AA	AA	aa	AA	AA	aa	AA	AA	AA	AA	AA	AA	aa	AA	AA	AA	aa	AA	aa
PA20	AA	aa	AA	aa	aa	aa	AA	-	aa	-	aa	aa	AA	-	aa	aa	aa	aa	AA	AA	aa	aa	AA	AA	aa	AA	AA
PA22	AA	aa	AA	AA	AA	AA	AA	AA	AA	AA	AA	AA	AA	aa	AA	AA	AA	AA	AA	AA	aa	AA	AA	AA	aa	AA	aa
PA22	AA	aa	aa	aa	aa	aa	AA	aa	aa	-	aa	aa	AA	aa	aa	aa	-	aa	aa	aa	aa	aa	aa	aa	aa	aa	aa
PA23	AA	aa	AA	AA	AA	AA	AA	AA	AA	AA	AA	AA	AA	aa	AA	AA	AA	AA	AA	AA	aa	AA	AA	AA	aa	AA	aa
PA23	AA	aa	aa	aa	aa	aa	AA	aa	aa	-	aa	aa	AA	aa	aa	aa	aa	aa	aa	aa	aa	aa	aa	aa	aa	aa	aa
PA28	AA	aa	AA	AA	AA	AA	AA	AA	AA	AA	AA	AA	AA	aa	AA	AA	AA	aa	AA	AA	AA	AA	AA	AA	AA	AA	aa
PA28	AA	aa	aa	aa	aa	aa	AA	aa	aa	-	aa	aa	AA	AA	AA	aa	aa	aa	AA	aa	aa	aa	aa	aa	AA	AA	AA
PA30	AA	aa	AA	AA	AA	aa	AA	aa	AA	AA	aa	aa	AA	aa	AA	AA	aa	aa	aa	AA	aa	AA	aa	aa	aa	AA	aa
PA30	AA	aa	aa	aa	aa	AA	AA	aa	aa	aa	aa	aa	AA	AA	aa	aa	aa	aa	aa	aa	aa	aa	aa	aa	aa	aa	aa
VA07	AA	aa	AA	AA	AA	AA	AA	AA	AA	AA	AA	AA	AA	aa	AA	AA	AA	aa	AA	aa	AA	AA	AA	AA	AA	AA	aa
VA07	AA	aa	aa	aa	aa	aa	AA	aa	aa	-	aa	aa	-	AA	AA	aa	aa	aa	aa	aa	aa	aa	aa	aa	aa	AA	AA
Va07	AA	aa	AA	-	AA	AA	AA	AA	AA	AA	AA	AA	AA	aa	AA	AA	AA	aa	AA	aa	AA	AA	AA	AA	AA	AA	aa
Va07	AA	aa	aa	aa	aa	aa	AA	aa	aa	-	aa	aa	AA	AA	AA	aa	aa	aa	aa	aa	aa	aa	aa	aa	aa	AA	AA

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[5]	YAO Xiao-Hua, WANG Yue, YAO You-Hua, AN Li-Kun, WANG Yan, WU Kun-Lun. Isolation and expression of a new gene HvMEL1 AGO in Tibetan hulless barley under leaf stripe stress [J]. Acta Agronomica Sinica, 2022, 48(5): 1181-1190.
[6]	FU Mei-Yu, XIONG Hong-Chun, ZHOU Chun-Yun, GUO Hui-Jun, XIE Yong-Dun, ZHAO Lin-Shu, GU Jia-Yu, ZHAO Shi-Rong, DING Yu-Ping, XU Yan-Hao, LIU Lu-Xiang. Genetic analysis of wheat dwarf mutant je0098 and molecular mapping of dwarfing gene [J]. Acta Agronomica Sinica, 2022, 48(3): 580-589.
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[10]	LI Jian-Ling, GONG Dan, WANG Su-Hua, CHEN Hong-Lin, CHENG Xu-Zhen, XIONG Tao, WANG Li-Xia. Construction of SNP high-density genetic map and QTL analysis of agronomic traits in cowpea (Vigna unguiculata (L.) Walp.) [J]. Acta Agronomica Sinica, 2022, 48(10): 2475-2482.
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