普通野生稻早抽穗基因OsEHD8的鉴定与进化分析

doi:10.3864/j.issn.0578-1752.2024.14.001

Abstract

Abstract:

【Objective】 The heading date plays a crucial role in influencing the regional adaptation and yield of rice (Oryza sativa L.). The identification of early heading genes contributes significantly to enhancing and fine-tuning the regulatory network that controls rice heading, which provides valuable genetic resources for molecular breeding with the goal of achieving early maturity and high yield in rice. 【Method】 CL33, a chromosome segment substitution line with early heading, and 93-11, its recipient parent with late heading, were used as research materials to investigate and analyze their major agronomic traits. Two DNA pools were constructed, comprising plants exhibiting extremely early and late heading. Whole-genome resequencing and BSA-Seq analyses were then conducted to locate the genomic region associated with the heading date. In the subsequent steps, InDel markers within this identified region were developed for fine mapping. The gene LOC-Os08g07740 emerged as the primary candidate gene within localization intervals, determined through gene prediction, candidate gene analyses, as well as references to relevant literatures. This candidate gene was subsequently cloned and analyzed for allelic variations. Moreover, we explored the genetic and phylogenetic relationships of the LOC_Os08g07740 gene within the three rice subgroups, Indica, Japonica and O. rufipogon. This analysis involved studying genomic data within approximately 40 kb upstream and downstream of the gene utilizing bioinformatics software.【Result】 Under both natural long-day and short-day conditions in Nanning, Guangxi, CL33 exhibited a 20-25 days shorter than its recipient parent 93-11. Moreover, under natural long-day conditions, the agronomic traits of CL33 were largely similar to those of 93-11, with the exception of a shortened spike length and a reduced number of grains per spike. Genetic analysis revealed that the early heading trait in CL33 was controlled by a recessive gene. This gene was finely localized within a 100 kb region between the markers PSM8-6 and PSM8-8 on the short arm of rice chromosome 8, encompassing 15 predicted candidate genes. Significantly, the candidate gene ORF13 (LOC_Os08g07740), which shared alleles with known heading date genes like DTH8/Ghd8 emerged as a key candidate. Sequencing and sequence alignment of ORF13 demonstrated an 888 bp coding sequence without introns, encoding a protein of 295 amino acids. Compared to the recipient parent 93-11, LOC_Os08g07740 in CL33 featured a 6 bp insertion and a 9 bp deletion between the 535-536th and 820-821st base pairs, respectively, resulting in consequential amino acid sequence alterations. Hence, it was tentatively named OsEHD8 as the target candidate gene. Genetic evolutionary analyses indicated a significant decrease in genetic diversity within the LOC_Os08g07740 gene in Indica and Japonica compared to O. rufipogon, with a 62.53% decrease in Indica and a 53.76% decrease in Japonica. Nevertheless, the differences in genetic diversity between Indica and Japonica were not statistically significant. The LOC_Os08g07740 gene featured a total of 13 haplotypes, with the Hap_2 possibly representing the common ancestor of the three subgroups. Geographical isolation or environmental differences might have led to the fixation of different haplotypes in the Indica and Japonica subgroups. These findings suggested that the LOC_Os08g07740 gene underwent directional selection in the three subgroups.【Conclusion】 OsEHD8, identified as a functional allele of DTH8/Ghd8, played a key role in promoting early heading in rice under both natural long-day and short-day conditions. Moreover, the chromosomal segment substitution line CL33, which carried the OsEHD8 allele, exhibited no significant differences in other agronomic traits compared to the recipient parent 93-11 under natural long-day conditions, except for a shorter spike length and a reduction in grains per spike.

Key words: rice (Oryza sativa L.), heading date, DTH8/Ghd8, BSA-seq, evolution

YAN LiuHui, ZHONG Qi, MA ZengFeng, WEI MinYi, LIU Chi, QIN YuanYuan, ZHOU XiaoLong, HUANG DaHui, LU YingPing, QIN Gang, ZHANG YueXiong. Identification and Evolutionary Analysis of the Early Heading Gene OsEHD8 in Common Wild Rice (Oryza rufipogon Giff.)[J].Scientia Agricultura Sinica, 2024, 57(14): 2703-2716.

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染色体 Chromosome	代换片段 Substitution segment	位置 Position (bp)	片段长度 Fragment length (bp)
1	--RM5365--	12264091-17274013	2504961
1	--RM315-RM472--	34949898-43207575	4706424
3	--RM175-RM282--	2454279-14694597	10390997
4	--RM3474-RM5320-RM7187-RM17308--	31845534-27015983	3444945
8	--RM5556-RM1309-RM8264--	3174356-19953040	16011747
11	--RM224--	25457233-26796502	669634

开放阅读框 Open reading frame	基因名称 Gene name	CDS物理位置 CDS physical position (bp)	CDS长度 CDS length (bp)	蛋白质长度 Protein length (aa)	预测功能 Putative function
ORF1	LOC_Os08g07620	4278359-4278688	330	109	表达蛋白Expressed protein
ORF2	LOC_Os08g07630	4283826-4284332	507	168	表达蛋白Expressed protein
ORF3	LOC_Os08g07640	4286407-4286820	414	137	表达蛋白Expressed protein
ORF4	LOC_Os08g07650	4289245-4289615	303	100	表达蛋白Expressed protein
ORF5	LOC_Os08g07660	4290418-4291283	549	182	表达蛋白Expressed protein
ORF6	LOC_Os08g07670	4293995-4294513	519	172	表达蛋白Expressed protein
ORF7	LOC_Os08g07680	4297225-4297737	444	147	表达蛋白Expressed protein
ORF8	LOC_Os08g07690	4300553-4301470	336	111	表达蛋白Expressed protein
ORF9	LOC_Os08g07700	4304696-4303902	528	175	表达AP2结构域蛋白 AP2 domain containing protein, expressed
ORF10	LOC_Os08g07710	4311784-4312071	288	95	假设蛋白Hypothetical protein
ORF11	LOC_Os08g07720	4318638-4316160	1449	482	预测表达的转移酶家族蛋白 Transferase family protein, putative, expressed
ORF12	LOC_Os08g07730	4325887-4329768	1410	469	预测表达的转移酶家族蛋白 Transferase family protein, putative, expressed
ORF13	LOC_Os08g07740	4335434-4333717	894	297	预测表达的类组氨酸转录因子 Histone-like transcription factor and archaeal histone, putative, expressed
ORF14	LOC_Os08g07760	4344171-4350502	1875	624	预测表达的BRI1相关受体激酶1 BRASSINOSTEROID INSENSITIVE 1- associated receptor kinase 1 precursor, putative, expressed
ORF15	LOC_Os08g07774	4352807-4361458	2397	798	预测表达的抗病蛋白RPM1 Disease resistance protein RPM1, putative, expressed

Identification and Evolutionary Analysis of the Early Heading Gene OsEHD8 in Common Wild Rice (Oryza rufipogon Giff.)

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