Development of molecular markers polymorphic between Dongxiang wild rice and 
            <i>Geng</i> rice cultivar ‘Nipponbare’

Ma, Xiaoding; Tang, Jinyu; Zhang, Jia-Ni; Cui, Di; Li, Hui; Li, Maomao; Han, Longzhi

doi:10.3724/sp.j.1006.2019.82037

Cited by 3 publications

(2 citation statements)

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“…With the rapid development of high-throughput sequencing technology and the decreasing cost of sequencing, the development of InDel markers by re-sequencing has increasingly been used in rice research. Shen Out of those markers, 203 were found to be polymorphisms between Dongxiang wild rice and Nipponbare, with an average distance of 1.9 Mb/locus [48]. However, most studies have concentrated on developing InDel markers between wild and cultivated rice or among subspecies, with only a few studies examining genome-wide InDel markers within the same subspecies.…”

Section: Development and Application Of Indel Markers In Rice Breedingmentioning

confidence: 99%

Genome-Wide Association Studies of Salt-Tolerance-Related Traits in Rice at the Seedling Stage Using InDel Markers Developed by the Genome Re-Sequencing of Japonica Rice Accessions

et al. 2023

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Japonica-specific markers are crucial for the analysis of genetic diversity, population structure, evolutionary traits, and genome-wide association study (GWAS) of japonica germplasm accessions. This study developed 402 insertion–deletion (InDel) polymorphic markers based on the re-sequencing of four japonica rice landraces and three japonica rice cultivars. These InDel markers were uniformly distributed across 12 rice chromosomes with high polymorphism and good amplification specificity. The average density of InDel markers on each chromosome was 0.95 Mb per locus. On the basis of these InDel markers, genetic diversity analyses and GWASs for 12 salt-tolerance-related traits were performed using 182 japonica rice accessions. In total, 1204 allelic variants were detected, with an average of 3.00 alleles and 2.10 effective alleles per locus. Based on population structure analysis, 182 japonica rice accessions were divided into four subgroups. The GWAS analyses revealed a total of 14 salt-tolerance-related InDels, which were located on chromosomes 1–5, 9, 10, and 12. Twenty-eight allelic loci were identified, explaining 6.83% to 11.22% of the phenotypic variance. Haplotype analysis detected six InDel markers associated with salt-tolerance-related traits that were significantly different (p < 0.05) or highly significantly different (p < 0.01) among different haplotypes. These markers can be utilized for the molecular identification of salt-tolerant rice germplasm accessions.

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Section: Development and Application Of Indel Markers In Rice Breedingmentioning

confidence: 99%

Genome-Wide Association Studies of Salt-Tolerance-Related Traits in Rice at the Seedling Stage Using InDel Markers Developed by the Genome Re-Sequencing of Japonica Rice Accessions

et al. 2023

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“…The QTLs controlling ME in the CSSLs were mapped by using previously reported genotypic data from our laboratory [28,29]. The CSL (QTL mapping in CSS lines) functionality was used to identify QTLs by the likelihood ratio test based on the stepwise regression for additive QTL (RSTEP-LRT-ADD) mapping method, which was developed for QTL mapping in nonideal or ideal CSSL populations [30].…”

Section: Genotypic Data Of the F 2 Segregating Population And Qtl Ana...mentioning

confidence: 99%

QTL Mapping of Mesocotyl Elongation and Confirmation of a QTL in Dongxiang Common Wild Rice in China

Huang

Cheng

et al. 2022

Agronomy

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Direct-seeded rice (DSR) cultivation is an effective and important way to resolve agricultural labor scarcity, water scarcity and high production cost issues. Mesocotyl elongation (ME) is the main driver of the rapid emergence of rice seedlings from the soil and is an important indicator of the suitability of rice varieties for direct seeding. Hence, discovering ME-related genes is particularly important for breeding rice varieties suitable for direct seeding. In this study, a chromosome segment substitution line (CSSL) population generated from a cross between Dongxiang common wild rice and Nipponbare (Nip) was used to map quantitative trait loci (QTLs) for ME. Two QTLs for mesocotyl length were identified on chromosomes 3 and 6 with logarithm of odds (LOD) scores ranging from 5.47 to 6.04 and explaining 15.95–16.79% of the phenotypic variance. Among these QTLs, qML6 accounted for the highest phenotypic variance (16.79%). Then, to confirm the strongest QTL, we generated an F2 segregating population via the CSL127 line harboring the qML6 locus and the recurrent parent Nip. The QTL qML6-1 associated with ME was mapped to a location between markers DX-C6-2 and DX-C6-4, which is consistent with the location of the previously mapped QTL qML6. qML6-1 had an LOD score of 8.45 and explained 30.56% of the phenotypic variance. The QTLs detected in this study provide promising targets for further genetic characterization and for use in marker-assisted selection to develop varieties with improved ME for the cultivation of DSR.

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Construction of chromosome segment substitution lines of Dongxiang common wild rice (Oryza rufipogon Griff.) in the background of the japonica rice cultivar Nipponbare (Oryza sativa L.)

Han

Tang

et al. 2019

Plant Physiology and Biochemistry

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Development of molecular markers polymorphic between Dongxiang wild rice and Geng rice cultivar ‘Nipponbare’

Cited by 3 publications

References 0 publications

Genome-Wide Association Studies of Salt-Tolerance-Related Traits in Rice at the Seedling Stage Using InDel Markers Developed by the Genome Re-Sequencing of Japonica Rice Accessions

Genome-Wide Association Studies of Salt-Tolerance-Related Traits in Rice at the Seedling Stage Using InDel Markers Developed by the Genome Re-Sequencing of Japonica Rice Accessions

QTL Mapping of Mesocotyl Elongation and Confirmation of a QTL in Dongxiang Common Wild Rice in China

Construction of chromosome segment substitution lines of Dongxiang common wild rice (Oryza rufipogon Griff.) in the background of the japonica rice cultivar Nipponbare (Oryza sativa L.)

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