Identification of a unique allele in the quantitative trait locus for crown root number in japonica rice from Japan using genome-wide association studies.

IF 2 4区 农林科学 Q2 AGRONOMY Breeding Science Pub Date : 2022-06-01 Epub Date: 2022-07-01 DOI:10.1270/jsbbs.22010
Shota Teramoto, Masanori Yamasaki, Yusaku Uga
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引用次数: 1

Abstract

To explore the genetic resources that could be utilized to help improve root system architecture phenotypes in rice (Oryza sativa), we have conducted genome-wide association studies to investigate maximum root length and crown root number in 135 10-day-old Japanese rice accessions grown hydroponically. We identified a quantitative trait locus for crown root number at approximately 32.7 Mbp on chromosome 4 and designated it qNCR1 (quantitative trait locus for Number of Crown Root 1). A linkage disequilibrium map around qNCR1 suggested that three candidate genes are involved in crown root number: a cullin (LOC_Os04g55030), a gibberellin 20 oxidase 8 (LOC_Os04g55070), and a cyclic nucleotide-gated ion channel (LOC_Os04g55080). The combination of haplotypes for each gene was designated as a haploblock, and haploblocks 1, 2, and 3 were defined. Compared to haploblock 1, the accessions with haploblocks 2 and 3 had fewer crown roots; approximately 5% and 10% reductions in 10-day-old plants and 15% and 25% reductions in 42-day-old plants, respectively. A Japanese leading variety Koshihikari and its progenies harbored haploblock 3. Their crown root number could potentially be improved using haploblocks 1 and 2.

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利用全基因组关联研究鉴定日本粳稻冠根数数量性状位点上的一个独特等位基因。
为了探索可以用于改善水稻根系结构表型的遗传资源,我们对135个水培10日龄日本水稻材料进行了全基因组关联研究,研究了最大根长和冠根数。我们在4号染色体上发现了一个约32.7 Mbp的冠根数数量性状位点,并将其命名为qNCR1(冠根数1的数量性状位点)。qNCR1周围的连锁不平衡图谱表明,三个候选基因参与了冠根数的控制:cullin (LOC_Os04g55030)、赤霉素20氧化酶8 (LOC_Os04g55070)和环核苷酸门控制离子通道(LOC_Os04g55080)。每个基因的单倍型组合被指定为一个单倍体,并定义了单倍体1、2和3。与单倍体块1相比,单倍体块2和3的冠根较少;10天大的植物分别减少约5%和10%,42天大的植物分别减少15%和25%。日本主要品种光光及其后代携带单倍体3。利用单倍体1和单倍体2可以提高冠根数。
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来源期刊
Breeding Science
Breeding Science 农林科学-农艺学
CiteScore
4.90
自引率
4.20%
发文量
37
审稿时长
1.5 months
期刊介绍: Breeding Science is published by the Japanese Society of Breeding. Breeding Science publishes research papers, notes and reviews related to breeding. Research Papers are standard original articles. Notes report new cultivars, breeding lines, germplasms, genetic stocks, mapping populations, database, software, and techniques significant and useful for breeding. Reviews summarize recent and historical events related breeding. Manuscripts should be submitted by corresponding author. Corresponding author must have obtained permission from all authors prior to submission. Correspondence, proofs, and charges of excess page and color figures should be handled by the corresponding author.
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