OsGA20ox1, a candidate gene for a major QTL controlling seedling vigor in rice

Abe, Akira; Takagi, Hiroki; Fujibe, Takahiro; Aya, Koichiro; Kojima, Mikiko; Sakakibara, Hitoshi; Uemura, Aiko; Matsuoka, Makoto; Terauchi, Ryohei

doi:10.1007/s00122-012-1857-z

Cited by 76 publications

(72 citation statements)

References 34 publications

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“…Takagi et al ([2013]) identified two QTLs for seedling vigor using 531 F 2 individuals of Dunghan Shali/Hitomebore. Two loci were confirmed to be close to the previously reported QTLs qPHS3-2S and qPHS-1 (Yano et al [2012]; Abe et al [2012b]). QTL-seq can generally be applied in population genomics studies to rapidly identify genomic regions that have undergone artificial or natural selective sweeps.…”

Section: Reviewsupporting

confidence: 78%

Application of resequencing to rice genomics, functional genomics and evolutionary analysis

Guo

Gao

Qian

2014

Rice

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Rice is a model system used for crop genomics studies. The completion of the rice genome draft sequences in 2002 not only accelerated functional genome studies, but also initiated a new era of resequencing rice genomes. Based on the reference genome in rice, next-generation sequencing (NGS) using the high-throughput sequencing system can efficiently accomplish whole genome resequencing of various genetic populations and diverse germplasm resources. Resequencing technology has been effectively utilized in evolutionary analysis, rice genomics and functional genomics studies. This technique is beneficial for both bridging the knowledge gap between genotype and phenotype and facilitating molecular breeding via gene design in rice. Here, we also discuss the limitation, application and future prospects of rice resequencing.

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Section: Reviewsupporting

confidence: 78%

Application of resequencing to rice genomics, functional genomics and evolutionary analysis

Guo

Gao

Qian

2014

Rice

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“…2014, Wang et al . 2010) and some QTLs were fine mapped to a narrow region and even cloned (Abe et al . 2012, Fujino et al .…”

Section: Discussionmentioning

confidence: 99%

Genetic analysis for rice seedling vigor and fine mapping of a major QTL <i>qSSL1b</i> for seedling shoot length

et al. 2017

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Seedling vigor is an important agricultural trait as direct-seeded rice technology becomes widely applied. In order to investigate the genetic mechanisms underlying seedling vigor in rice, seeds of 132 recombinant inbred lines (RILs) derived from 93-11 and PA64s, harvested from Lingshui and Hangzhou were cultivated in the nutrient solution, and four indices for seedling vigor were measured including seedling shoot length (SSL), seedling root length (SRL), seedling wet weight (SWW) and seedling dry weight (SDW). Significant correlations were observed among the indices, and also between 1000-seed weight (TSW) and SWW or SDW. Combined with a high-resolution genetic map generated from sequencing of the RILs, 65 quantitative trait loci (QTLs) were detected on all chromosomes with interval of 1.93 Mb on average. Among 57 QTLs for seedling vigor, 28 were detected from seeds harvested in both sites and 33 were first identified. With BC3F2 derived from 93-11 and a CSSL harboring segments from PA64s in 93-11 background, a major QTL for SSL, qSSL1b was fine mapped within 80.5 kb between two InDel markers. Our study provides a platform for further cloning of the QTL and dissecting the molecular basis for seedling vigor at early seedling stage in rice.

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“…A very small number of studies have been reported in which populations derived from intrasubspecific crosses have been analyzed. These include indica/indica (Cui et al 2002;Xie et al 2014) and japonica/japonica (Yang et al 2010;Abe et al 2012) crosses. More recently, association mapping strategies have been employed to detect seedling vigor QTL in natural populations of rice varieties (primarily indica) and landraces (Dang et al 2014;Cheng et al 2015;Wu et al 2015;Anandan et al 2016;Lu et al 2016).…”

Section: Introductionmentioning

confidence: 99%

Identification of Seedling Vigor-Associated Quantitative Trait Loci in Temperate Japonica Rice

Cordero-Lara¹,

Kim²,

Tai³

2016

Plant Breed. Biotech.

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A quantitative trait loci (QTL) analysis of seedling vigor traits was conducted under dry-seeded conditions using 176 recombinant inbred lines developed from a cross of two California temperate japonica rice varieties M-203 and M-206. Height at early seedling (HES) and height at late seedling (HLS) stage, growth rate (GR), and fresh weight were evaluated in a growth chamber. Assessment of HES, HLS, and GR was also performed in outdoor basins in 2015 and 2016. M-203 was significantly better for all traits in the growth chamber, however, no significant differences were observed between the parents in the outdoor basins with the exception of HES in 2015. Genotyping by sequencing was used to construct a map of ＞6,000 single nucleotide polymorphisms. Six QTL were detected in the growth chamber, one each on chromosomes 2, 9, 10, and 12 and two at the same position on 1. qFW1 and qHES1 explain 34.6% and 8.7% of the phenotypic variation observed for their respective traits and correspond to previously reported QTL for shoot length. All positive effects were contributed by the M-203 allele except for the qHLS12. Two QTL, qHES8 (12.3%; M-206 allele) and qHES9 (9.4%; M-203 allele), were detected in the outdoor basin 2016, but none in 2015. RIL-187 was consistently among the highest vigor lines in all environments and additional evaluations confirmed this finding. The molecular and genetic resources developed here will facilitate further investigation of seedling vigor and breeding of enhanced temperate japonica rice varieties.

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OsGA20ox1, a candidate gene for a major QTL controlling seedling vigor in rice

Cited by 76 publications

References 34 publications

Application of resequencing to rice genomics, functional genomics and evolutionary analysis

Application of resequencing to rice genomics, functional genomics and evolutionary analysis

Genetic analysis for rice seedling vigor and fine mapping of a major QTL <i>qSSL1b</i> for seedling shoot length

Identification of Seedling Vigor-Associated Quantitative Trait Loci in Temperate Japonica Rice

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