Genetic analysis for rice seedling vigor and fine mapping of a major QTL &lt;i&gt;qSSL1b&lt;/i&gt; for seedling shoot length

Zhang, Anpeng; Liu, Chaolei; Chen, Guang; Hong, Kai; Gao, Yang; Tian, Peng; Peng, Youlin; Zhang, Bin; Ruan, Banpu; Jiang, Hongzhen; Guo, Longbiao; Qian, Qian; Gao, Zhenyu

doi:10.1270/jsbbs.16195

Cited by 38 publications

(30 citation statements)

References 27 publications

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“…Therefore, root phenotypes are important phenotypic indicators. However, most researchers in previous reports investigating seedling roots adopted indexes related to only the maximum RL and root weight (Zhang et al, 2005;Diwan et al, 2013;Dang et al, 2014;Zhang et al, 2017;Singh et al, 2017). In this study, we collected total RL, RSA, RV, RD and RFW data, which can not only provide in-depth seedling roots detail of but also improve the efficiency of mapping.…”

Section: Discussionmentioning

confidence: 99%

“…Seedling vigor is controlled by many QTLs and is also one of several important agronomic traits for direct-seeding rice systems (Yano et al, 2012). During the last few decades, a large number of QTLs associated with seedling vigor have been identified (Cui et al, 2002;Zhang et al, 2005;Lu et al, 2007;Zhou et al, 2007;Cairns et al, 2009;Abe et al, 2012;Yano et al, 2012;Cheng et al, 2013;Diwan et al, 2013;Dang et al, 2014;Cordero-Lara et al, 2016;Singh et al, 2017;Zhang et al, 2017). Among these QTLs, only one major QTL for seedling height (SH) on the long arm of chromosome 3 has been finely mapped, and OsGA20ox1 is the most likely candidate gene at this locus (Abe et al, 2012;Yano et al, 2012).…”

Section: Introductionmentioning

confidence: 99%

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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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Section: Discussionmentioning

confidence: 99%

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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“…Seedling vigour QTLs have been identified using biparental mapping populations (Cheng et al, ; Cui et al, ; Zhang, Qu, Wan, Chen, & Zhu, ; Zhou et al, ), recombinant inbred lines (Singh et al, ; Zhang et al, ), and association mapping studies (Dang et al, ). Still, an understanding of the physiological mechanisms underlying the QTLs is often lacking, and candidate gene identification has proved challenging due to complexity and quantitative inheritance, as well as strong genotype‐environment interactions (Mahender et al, ).…”

Section: Introductionmentioning

confidence: 99%

Genome‐wide association and gene validation studies for early root vigour to improve direct seeding of rice

Wang

Longkumer

Catausan

et al. 2018

Plant Cell & Environment

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Elucidation of the genetic control of rice seedling vigour is now paramount with global shifts towards direct seeding of rice and the consequent demand for early vigour traits in breeding programmes. In a genome-wide association study using an indica-predominant diversity panel, we identified quantitative trait loci (QTLs) for root length and root number in rice seedlings. Among the identified QTLs, one QTL for lateral root number on chromosome 11, qTIPS-11, was associated with a 32.4% increase in lateral root number. The locus was validated in independent backgrounds, and a predicted glycosyl hydrolase, TIPS-11-9, was identified as the causal gene for observed phenotypic differences. TIPS-11-9 was differentially expressed in emerging lateral roots of contrasting qTIPS-11 haplotypes, which was likely due to differences in cis-regulatory elements and auxin responsiveness. Abolishment of Tips-11-9 function through T-DNA insertion in a qTIPS-11-positive background resulted in a reduction of lateral root number, which negatively affected biomass accumulation, particularly under phosphorous-limiting conditions. Marker-assisted introgression of qTIPS-11 into modern indica varieties will aid in the generation of varieties adapted to direct seeding and thus facilitate the adoption of direct seeding practices in tropical Asia.

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“…In this study, we evaluated seedling vigor by measuring SH, RL, LL, LW, SFW, RFW, SDW, and R:S, as these traits are considered to be representative indicators of seedling vigor (Redoña and Mackill 1996a, 1996b, Regan et al 1992, Zhang et al 2017. We focused on the first 25 days after germination before independent photosynthesis is fully established; in this time, therefore, main nutrients and ener- primary screening tool in breeding populations.…”

Section: Discussionmentioning

confidence: 99%

Novel haplotype combinations reveal enhanced seedling vigor traits in rice that can accurately predict dry biomass accumulation in seedlings

Guo

You

et al. 2019

Breed. Sci.

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Seedling vigor is of vital importance for the initial plant establishment of direct-seeded rice. Here, 166 recombinant inbred lines were employed to assess eight seedling vigor traits over the first 25 days of germination. Significant correlations were found between most traits, and statistical analysis has revealed, for the first time, a linear relationship that uses seedling height and fresh weight to accurately predict the accumulation of dry biomass. Further, a subset of 20 lines, spanning the phenotypic range of the larger population, were genotyped by using 16 simple sequence repeats (SSR) markers known to be associated with seedling vigor traits. Markers RM317 and RM348 linked with significantly different phenotypes, including seedling height and fresh weight. One combination, haplotype II-1 (RM317 (I/II) and RM348 (1/2)), consistently produced superior values for seedling height, root length, and leaf length. The new prediction tool for seedling dry weight, namely the haplotype of RM317 and RM348, will have a wide range of applications in breeding strategies by using markerassisted selection to produce elite lines that optimize genetic composition contributing to seedling vigor.

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

Cited by 38 publications

References 27 publications

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

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

Genome‐wide association and gene validation studies for early root vigour to improve direct seeding of rice

Novel haplotype combinations reveal enhanced seedling vigor traits in rice that can accurately predict dry biomass accumulation in seedlings

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