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

作物学报 ›› 2022, Vol. 48 ›› Issue (10): 2463-2474.doi: 10.3724/SP.J.1006.2022.11071

• 作物遗传育种·种质资源·分子遗传学 • 上一篇下一篇

青稞早抽穗主效QTL cqHD2H-2的遗传定位及候选基因分析

余鑫莲(), 李新(), 姚晓华, 姚有华, 白羿雄, 安立昆, 吴昆仑()

青海大学农林科学院 / 青海省青稞遗传育种重点实验室 / 国家麦类改良中心青海青稞分中心, 青海西宁810016

收稿日期:2021-08-11 接受日期:2022-02-25 出版日期:2022-10-12 网络出版日期:2022-04-01
通讯作者: 吴昆仑
作者简介:第一作者联系方式: 余鑫莲, E-mail: yuxl1777@163.com;
李新, E-mail: lixinyynq@163.com第一联系人：
^** 同等贡献
基金资助:
青海省自然科学基金项目(2021-ZJ-950Q);国家自然科学基金项目(32160493);财政部和农业农村部国家现代农业产业技术体系建设专项(CAS-05)

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

YU Xin-Lian(), LI Xin(), YAO Xiao-Hua, YAO You-Hua, BAI Yi-Xiong, AN Li-Kun, WU Kun-Lun()

Agriculture and Forestry Academy, Qinghai University / Qinghai Key Laboratory of Hulless Barley Genetics and Breeding / Hulless Barley Branch of State Wheat Improvement Centre, Xining 810016, Qinghai, China

Received:2021-08-11 Accepted:2022-02-25 Published:2022-10-12 Published online:2022-04-01
Contact: WU Kun-Lun
About author:First author contact:
^** Contributed equally to this work
Supported by:
Natural Science Foundation Project of Qinghai Province(2021-ZJ-950Q);National Natural Science Foundation of China(32160493);China Agriculture Research System of MOF and MARA(CAS-05)

摘要/Abstract

摘要：

抽穗期是决定青稞品种的种植区域范围和季节适应性的重要农艺性状, 也是青稞成熟早晚的关键标志。在前期实验中, 青稞早抽穗主效QTL cqHD2H-2被定位于青稞2H染色体上约84 Mb的区间内, 为进一步验证该位点的有效稳定性, 本研究对cqHD2H-2进行定位验证及候选基因分析。利用早抽穗青稞品种DZZ与晚抽穗青稞品种KL10构建F₅群体, 在cqHD2H-2区段内开发InDel标记, 共筛选到3个与目标基因紧密连锁的分子标记, 扫描F₅群体中的25株极端早抽穗和25株极端晚抽穗单株, 获得1个侧翼共显性标记, 将cqHD2H-2进一步限定在标记PA22和Va07之间约40 Mb的区间内。该区段通过与大麦及水稻同源共线性比对, 筛选到水稻抽穗期基因DTH8在大麦中的同源基因HORVU2Hr1G087460 (HvNF-YB3)。比较HvNF-YB3基因全长, 发现Hv2H.NF-YB3 (DZZ)与Hv2H.nf-yb3 (KL10)编码区由1个外显子组成, 编码区为750 bp, 启动子区为2116 bp, Hv2H.NF-YB3与Hv2H.nf-yb3启动子区存在3个SNPs。Hv2H.NF-YB3与Hv2H.nf-yb3的表达分析表明, Hv2H.NF-YB3与Hv2H.nf-yb3在转录水平上存在显著差异, Hv2H.NF-YB3与Hv2H.nf-yb3在茎、芒和颖壳组织中均有表达, 但相较于Hv2H.NF-YB3, Hv2H.nf-yb3在各组织中的表达量均显著下降, 且二者随着生育期的推进, 表达量均依次降低。因此, Hv2H.NF-YB3可能在青稞抽穗时间调控中发挥作用。本研究为青稞早抽穗分子标记辅助选择育种体系的建立及目标基因的图位克隆奠定了基础。

关键词: 青稞, cqHD2H-2, 分子标记, 遗传图谱, HvNF-YB3

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

余鑫莲, 李新, 姚晓华, 姚有华, 白羿雄, 安立昆, 吴昆仑. 青稞早抽穗主效QTL cqHD2H-2的遗传定位及候选基因分析[J]. 作物学报, 2022, 48(10): 2463-2474.

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.

图/表 8

表1

图1

表2

图2

图3

图4

表3

Hv2H.NF-YB3启动子区元件分析"

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

表3

图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

青稞早抽穗主效QTL cqHD2H-2的遗传定位及候选基因分析

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
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