Mapping of quantitative trait loci controlling seedling vigor in rice (Oryza sativa L.) under submergence

Manangkil, Oliver Escaño; Vu, Hien Thi Thu; Mori, Naoki; Yoshida, Shigeo; Nakamura, Chiharu

doi:10.1007/s10681-012-0857-z

Cited by 21 publications

(16 citation statements)

References 45 publications

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“…All of the unique alleles were detected in the gene pools of traditional varieties (V10 and V22 from Central Delta and V6, V8, V15, V25 and V26 from Red River Delta in Tables 1 and 3). A possible relationship of these unique alleles with quantitative trait locus (QTL) regions associated with seedling vigour under submergence in rice [7] must be studied.…”

Section: Pic Value and Unique Allelesmentioning

confidence: 99%

“…[2À5] This trait is particularly important for optimum stand establishment during early seedling stages in the direct-seeding rice cultivation system in paddy field. [6,7] Seedling vigour is a complex trait influenced by the interaction between many genes and environmental conditions. [8] Genetic diversity is a prerequisite and a vital resource for plant breeders to improve the effective breeding programmes.…”

Section: Introductionmentioning

confidence: 99%

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Genetic diversity of Vietnamese lowland rice germplasms as revealed by SSR markers in relation to seedling vigour under submergence

Nguyen

Khanh

et al. 2015

Biotechnology & Biotechnological Equipment

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In the direct-seeding rice cultivation system, seedling vigour is one of the most important traits for stable stand establishment during early seedling stages, particularly under submergence that is caused by temporal flash flood. We studied the genetic diversity in a set of 40 Vietnamese lowland rice varieties using 30 simple sequence repeat (SSR) markers covering all rice chromosomes. A total of 111 alleles were detected, with a mean of 3.7 alleles per locus. The number of polymorphic alleles detected by each SSR marker ranged from 2 to 6. The fragment size of a given SSR locus varied between 85 and 650 bp and the frequency of a major allele at each locus ranged from 32.5% to 76.9%. Polymorphism information content value varied from 0.355 to 0.774 with an average of 0.594. The genetic similarity calculated between pairs of rice varieties ranged from 0.03 to 0.97 with an average of 0.27. According to a constructed dendrogram of unweighted pair group method with arithmetic mean based on the SSR marker analysis, the tested rice varieties were clustered into two major groups consisting of five subgroups. Significant correlations existed between the mean genetic similarity and the mean seedling vigour estimated by shoot length under submergence among the tested varieties. Our results suggested usefulness of the SSR marker system to assess genetic diversity in Vietnamese rice germplasms in relation to their seedling vigour under submergence.

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Section: Pic Value and Unique Allelesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genetic diversity of Vietnamese lowland rice germplasms as revealed by SSR markers in relation to seedling vigour under submergence

Nguyen

Khanh

et al. 2015

Biotechnology & Biotechnological Equipment

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“…RM525 on chromosome 2 is located in the region (28292005-28,292,040 bp) in which a QTL for seedling dry weight has been detected by Han et al, (2007) [42]. RM232 on chromosome 3 is located in the region (15644275-15,646,800 bp) in which a QTLs for germination rate, seed weight, shoot length and root length has been detected in different studies [43][44][45]. RM434 on chromosome 9 is located in the region (15662573-15,662, 838 bp) in which a QTLs for seedling dry weight has been detected in different studies [9,43].…”

Section: Discussionmentioning

confidence: 99%

Mining of favorable alleles for seed reserve utilization efficiency in Oryza sativa by means of association mapping

Ali

Eltahawy

et al. 2020

BMC Genet

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Background: Wet direct-seeded rice is a possible alternative to conventional puddled transplanted rice; the former uses less water and reduces labor requirements. Improving seed reserve utilization efficiency (SRUE) is a key factor in facilitating the application of this technology. However, the QTLs controlling this trait are poorly investigated. In this study, a genome-wide association study (GWAS) was conducted using a natural population composed of 542 accessions of rice (Oryza sativa L.) which were genotyped using 266 SSR markers. Large phenotypic variations in SRUE were found in the studied population. Results: The average SRUE over 542 accessions across two years (2016 and 2017) was 0.52 mg.mg − 1 , ranging from 0.22 mg.mg-1 to 0.93 mg.mg − 1 , with a coefficient of variation of 22.66%. Overall, 2879 marker alleles were detected in the population by 266 pairs of SSR markers, indicating a large genetic variation existing in the population. Using general linear model method, 13 SSR marker loci associated with SRUE were detected and two (RM7309 and RM434) of the 13 loci, were also detected using mixed linear model analyses, with percentage of phenotypic variation explained (PVE) greater than 5% across two years. The 13 association loci (P < 0.01) were located on all chromosomes except chromosome 11, with PVE ranging from 5.05% (RM5158 on chromosome 5) to 12% (RM297 on chromosome 1). Association loci RM7309 on chromosome 6 and RM434 on chromosome 9 revealed by both models were detected in both years. Twenty-three favorable alleles were identified with phenotypic effect values (PEV) ranging from 0.10 mg.mg − 1 (RM7309-135 bp on chromosome 9) to 0.45 mg.mg − 1 (RM297-180 bp on chromosome 2). RM297-180 bp showed the largest phenotypic effect value (0.44 mg.mg − 1 in 2016 and 0.45 mg.mg − 1 in 2017) with 6.72% of the accessions carrying this allele and the typical carrier accession was Manyedao, followed by RM297-175 bp (0.43 mg.mg − 1 in 2016 and 0.44 mg.mg − 1 in 2017). Conclusion: Nine novel association loci for SRUE were identified, compared with previous studies. The optimal parental combinations for pyramiding more favorable alleles for SRUE were selected and could be used for breeding rice accessions suitable for wet direct seeding in the future.

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“…A test-tube method developed and successfully used in rice [36][37][38][39] was adopted to study seed germination and seedling growth. Aged and non-aged seeds of NC hybrids and CS were imbibed individually for 2 days in glass test-tubes (inner diameter of 14 mm, height of 165 mm) filled with 15 mL of deionized water (10 cm in depth).…”

Section: Bioassay Methods For Assessing Seed Germination and Seedling mentioning

confidence: 99%

Differential and interactive effects of cytoplasmic substitution and seed ageing on submergence stress response in wheat (Triticum aestivum L.)

Takenaka

Yamamoto

Nakamura

2018

Biotechnology & Biotechnological Equipment

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Cytoplasmic genomes affect various phenotypes, including abiotic stress responses, through interaction with nuclear genomes in plants. We focused on the effects of cytoplasmic substitution on germination and seedling growth in combinations with submergence and seed ageing, both of which are known to inhibit these traits posing a challenge in agriculture and seed banking. We carried out comparative phenotypic studies of submergence and seed ageing effects using a series of nucleus-cytoplasm (NC) hybrids of wheat, in which 11 heterologous cytoplasms of Triticum and Aegilops species were combined with a common nucleus. Adopting the testtube bioassay, germination and seedling growth were studied using aged and non-aged seeds. Imbibed seeds were subjected to 3-days submergence followed by incubation under de-submergence conditions. Seed ageing reduced the germination rates in NC hybrids. Submergence and seed ageing both caused reduction of seedling growth evaluated by shoot length in all or most of the lines. The magnitude of shoot growth inhibition by submergence and seed ageing varied greatly among NC hybrids compared with the nuclear donor, and three distinct response types were recognized. Submergence and seed ageing, in combination, caused leaf chlorosis in most of NC hybrids. Our results suggested that the observed diverse effects of cytoplasmic substitution were exerted through differential interactions with submergence and seed ageing. Further studies are needed to clarify the mechanisms underlying cytoplasmic genome diversity and interaction with nuclear genomes affecting submergence and seed ageing responses in wheat. ARTICLE HISTORY

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Mapping of quantitative trait loci controlling seedling vigor in rice (Oryza sativa L.) under submergence

Cited by 21 publications

References 45 publications

Genetic diversity of Vietnamese lowland rice germplasms as revealed by SSR markers in relation to seedling vigour under submergence

Genetic diversity of Vietnamese lowland rice germplasms as revealed by SSR markers in relation to seedling vigour under submergence

Mining of favorable alleles for seed reserve utilization efficiency in Oryza sativa by means of association mapping

Differential and interactive effects of cytoplasmic substitution and seed ageing on submergence stress response in wheat (Triticum aestivum L.)

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