Combined strategy employing MutMap and RNA-seq reveals genomic regions and genes associated with complete panicle exsertion in rice.

IF 2.6 3区农林科学 Q1 AGRONOMY

Molecular Breeding Pub Date : 2023-08-22 eCollection Date: 2023-09-01 DOI:10.1007/s11032-023-01412-1

Anil A Hake, Suneel Ballichatla, Kalyani M Barbadikar, Nakul Magar, Shubhankar Dutta, C G Gokulan, Komal Awalellu, Hitendra K Patel, Ramesh V Sonti, Amol S Phule, Embadi Prashanth Varma, Pradeep Goud Ayeella, Poloju Vamshi, R M Sundaram, Sheshu Madhav Maganti

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Abstract

Complete panicle exsertion (CPE) in rice is an important determinant of yield and a desirable trait in breeding. However, the genetic basis of CPE in rice still remains to be completely characterized. An ethyl methane sulfonate (EMS) mutant line of an elite cultivar Samba Mahsuri (BPT 5204), displaying stable and consistent CPE, was identified and named as CPE-110. MutMap and RNA-seq were deployed for unraveling the genomic regions, genes, and markers associated with CPE. Two major genomic intervals, on chromosome 8 (25668481-25750456) and on chromosome 11 (20147154-20190400), were identified to be linked to CPE through MutMap. A non-synonymous SNP (G/A; Chr8:25683828) in the gene LOC_Os08g40570 encoding pyridoxamine 5'-phosphate oxidase with the SNP index 1 was converted to Kompetitive allele-specific PCR (KASP) marker. This SNP (KASP 8-1) exhibited significant association with CPE and further validated through assay in the F₂ mapping population, released varieties and CPE exhibiting BPT 5204 mutant lines. RNA-seq of the flag leaves at the booting stage, 1100 genes were upregulated and 1305 downregulated differentially in CPE-110 and BPT 5204. Metabolic pathway analysis indicated an enrichment of genes involved in photosynthesis, glyoxylate, dicarboxylate, porphyrin, pyruvate, chlorophyll, carotenoid, and carbon metabolism. Further molecular and functional studies of the candidate genes could reveal the mechanistic aspects of CPE.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-023-01412-1.

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MutMap和RNA-seq的联合策略揭示了水稻与完全穗外露相关的基因组区域和基因。

水稻全穗外露（CPE）是决定产量的重要因素，也是育种的理想性状。然而，水稻CPE的遗传基础仍有待完全鉴定。从优良品种Samba Mahsuri（BPT 5204）中鉴定出一株表现出稳定一致CPE的甲烷磺酸乙酯（EMS）突变体系，命名为CPE-110。MutMap和RNA-seq用于解开与CPE相关的基因组区域、基因和标记。通过MutMap鉴定出8号染色体（25668481-25750456）和11号染色体（20147154-20190400）上的两个主要基因组区间与CPE相关。编码SNP指数为1的吡哆胺5'-磷酸氧化酶的基因LOC_Os08g40570中的非同义SNP（G/A；Chr8:25683828）被转化为竞争性等位基因特异性PCR（KASP）标记。该SNP（KASP 8-1）表现出与CPE的显著相关性，并通过在F2定位群体、释放的品种和表现出BPT 5204突变系的CPE中的测定进一步验证。孕穗期旗叶的RNA-seq，在CPE-110和BPT 5204中，1100个基因上调，1305个基因下调。代谢途径分析表明，参与光合作用、乙醛酸盐、二羧酸盐、卟啉、丙酮酸盐、叶绿素、类胡萝卜素和碳代谢的基因富集。对候选基因进行进一步的分子和功能研究可以揭示CPE的机制。补充信息：在线版本包含补充材料，可访问10.1007/s11032-023-01412-1。

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来源期刊

Molecular Breeding 农林科学-农艺学

CiteScore

5.60

自引率

6.50%

发文量

审稿时长

1.5 months

期刊介绍： Molecular Breeding is an international journal publishing papers on applications of plant molecular biology, i.e., research most likely leading to practical applications. The practical applications might relate to the Developing as well as the industrialised World and have demonstrable benefits for the seed industry, farmers, processing industry, the environment and the consumer. All papers published should contribute to the understanding and progress of modern plant breeding, encompassing the scientific disciplines of molecular biology, biochemistry, genetics, physiology, pathology, plant breeding, and ecology among others. Molecular Breeding welcomes the following categories of papers: full papers, short communications, papers describing novel methods and review papers. All submission will be subject to peer review ensuring the highest possible scientific quality standards. Molecular Breeding core areas: Molecular Breeding will consider manuscripts describing contemporary methods of molecular genetics and genomic analysis, structural and functional genomics in crops, proteomics and metabolic profiling, abiotic stress and field evaluation of transgenic crops containing particular traits. Manuscripts on marker assisted breeding are also of major interest, in particular novel approaches and new results of marker assisted breeding, QTL cloning, integration of conventional and marker assisted breeding, and QTL studies in crop plants.