Association mapping of seed germination and seedling growth at three conditions in indica rice (Oryza sativa L.)

Jiaan, Cheng; He, Yuqing; Yang, Bin; Lai, Yanyan; Wang, Zhoufei; Zhang, Hongsheng

doi:10.1007/s10681-015-1477-1

Cited by 28 publications

(36 citation statements)

References 54 publications

(60 reference statements)

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“…Previous studies have shown that salinity tolerance is developmentally regulated and growth stage-specific in rice (Cheng et al, 2015). Therefore, the development of rice varieties with vigorous germination and seedling growth simultaneously under salinity stress is difficult.…”

Section: Discussionmentioning

confidence: 99%

A quantitative trait locus,qSE3, promotes seed germination and seedling establishment under salinity stress in rice

et al. 2019

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SummarySeed germination is a complex trait determined by both quantitative trait loci (QTLs) and environmental factors and also their interactions. In this study, we mapped one major QTL qSE3 for seed germination and seedling establishment under salinity stress in rice. To understand the molecular basis of this QTL, we isolated qSE3 by map‐based cloning and found that it encodes a K+ transporter gene, OsHAK21. The expression of qSE3 was significantly upregulated by salinity stress in germinating seeds. Physiological analysis suggested that qSE3 significantly increased K+ and Na+ uptake in germinating seeds under salinity stress, resulting in increased abscisic acid (ABA) biosynthesis and activated ABA signaling responses. Furthermore, qSE3 significantly decreased the H2O2 level in germinating seeds under salinity stress. All of these seed physiological changes modulated by qSE3 might contribute to seed germination and seedling establishment under salinity stress. Based on analysis of single‐nucleotide polymorphism data of rice accessions, we identified a HAP3 haplotype of qSE3 that was positively correlated with seed germination under salinity stress. This study provides important insights into the roles of qSE3 in seed germination and seedling establishment under salinity stress and facilitates the practical use of qSE3 in rice breeding.

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Section: Discussionmentioning

confidence: 99%

A quantitative trait locus,qSE3, promotes seed germination and seedling establishment under salinity stress in rice

et al. 2019

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“…Seed germination is a complex process that can be influenced by many factors, such as seed size, genotype, seed development, storage time and environment (Sun et al, 2007;Milošević et al, 2010). To date, numerous quantitative trait loci (QTLs) for seed germination have been reported in rice (Miura et al, 2002;Fujino et al, 2004;Jiang et al, 2006;Fujino et al, 2008;Wang et al, 2010;Li et al, 2013;Liu et al, 2014;Xie et al, 2014;Cheng et al, 2015;Hsu and Tung, 2015;Kretzschmar et al, 2015;Jiang et al, 2017;Wang et al, 2017;Jin et al, 2018). However, cloned genes related to the control of rice seed germination are still rare.…”

Section: Introductionmentioning

confidence: 99%

Quantitative Trait Locus Analysis of Seed Germination and Early Seedling Growth in Rice

Yang

et al. 2019

Front. Plant Sci.

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Seed germination and early seedling growth are important agricultural traits for developing populations of both irrigated and directly seeded rice (DSR). To investigate the genetic mechanisms underlying seed germination and early seedling growth in rice, 275 recombinant inbred lines (RILs) were genotyped in this study via the genotyping-bysequencing (GBS) approach to construct a high-density linkage bin map based on the parent-independent genotyping method. Quantitative trait loci (QTLs) for 12 traits related to seed germination and early seedling growth were analyzed. Totally, 22 additive loci were detected, after analysis of the interaction between additive QTLs and environments, five stable additive loci were obtained. Among them, loci 4, 5, 12 and 14 exhibited clear pleiotropic effects that were associated with multiple traits. Analysis of the effects of the five additive stable loci showed that a single locus increased the corresponding phenotypic value. Ten of the 275 RILs pyramided the excellent alleles of the five stable genetic loci. Most phenotypic values of the ten RILs were greater than the average values. Four RILs (G260, G342, G371, and G401) with more excellent phenotypic values were subsequently selected; these RILs could serve as donor parents of favorable alleles in the breeding process. Due to the existence of pleiotropy, the use of these genetic loci for pyramid breeding can further increase the efficiency to reach breeding goals. In addition, these five stable loci have an average physical interval of only 170 kb, we also further identified five promising candidate genes by qRT-PCR, which provides us with a basis for future cloning of these genes. Overall, this work will help broaden our understanding of the genetic control of seed germination and early seedling growth, and this study provides both a good theoretical basis and a new genetic resource for the breeding of direct-seeded rice.

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“…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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Association mapping of seed germination and seedling growth at three conditions in indica rice (Oryza sativa L.)

Cited by 28 publications

References 54 publications

A quantitative trait locus,qSE3, promotes seed germination and seedling establishment under salinity stress in rice

A quantitative trait locus,qSE3, promotes seed germination and seedling establishment under salinity stress in rice

Quantitative Trait Locus Analysis of Seed Germination and Early Seedling Growth in Rice

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

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