Genetic Diversity of Wild Rice Species in Yunnan Province of China

Cheng, Zhihui; Ying, F.; Ding-qing, LI; Yu, Tong; Fu, Jian; Yan, Huijun; Zhang, Dunyu; Li, Wei-jiao; Huang, Xing-Qi

doi:10.1016/s1672-6308(12)60016-x

Cited by 9 publications

(5 citation statements)

References 4 publications

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“…As genetic diversity among commercial cultivars has declined, it is difficult to find new resistance genes from existing cultivars for the further improvement of rice. Therefore, sufficient resistance could be managed by exploring wild species [ 6 ].…”

Section: Introductionmentioning

confidence: 99%

Genome wide re-sequencing of newly developed Rice Lines from common wild rice (Oryza rufipogon Griff.) for the identification of NBS-LRR genes

Wen

Ghouri

et al. 2017

PLoS ONE

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Common wild rice (Oryza rufipogon Griff.) is an important germplasm for rice breeding, which contains many resistance genes. Re-sequencing provides an unprecedented opportunity to explore the abundant useful genes at whole genome level. Here, we identified the nucleotide-binding site leucine-rich repeat (NBS-LRR) encoding genes by re-sequencing of two wild rice lines (i.e. Huaye 1 and Huaye 2) that were developed from common wild rice. We obtained 128 to 147 million reads with approximately 32.5-fold coverage depth, and uniquely covered more than 89.6% (> = 1 fold) of reference genomes. Two wild rice lines showed high SNP (single-nucleotide polymorphisms) variation rate in 12 chromosomes against the reference genomes of Nipponbare (japonica cultivar) and 93–11 (indica cultivar). InDels (insertion/deletion polymorphisms) count-length distribution exhibited normal distribution in the two lines, and most of the InDels were ranged from -5 to 5 bp. With reference to the Nipponbare genome sequence, we detected a total of 1,209,308 SNPs, 161,117 InDels and 4,192 SVs (structural variations) in Huaye 1, and 1,387,959 SNPs, 180,226 InDels and 5,305 SVs in Huaye 2. A total of 44.9% and 46.9% genes exhibited sequence variations in two wild rice lines compared to the Nipponbare and 93–11 reference genomes, respectively. Analysis of NBS-LRR mutant candidate genes showed that they were mainly distributed on chromosome 11, and NBS domain was more conserved than LRR domain in both wild rice lines. NBS genes depicted higher levels of genetic diversity in Huaye 1 than that found in Huaye 2. Furthermore, protein-protein interaction analysis showed that NBS genes mostly interacted with the cytochrome C protein (Os05g0420600, Os01g0885000 and BGIOSGA038922), while some NBS genes interacted with heat shock protein, DNA-binding activity, Phosphoinositide 3-kinase and a coiled coil region. We explored abundant NBS-LRR encoding genes in two common wild rice lines through genome wide re-sequencing, which proved to be a useful tool to exploit elite NBS-LRR genes in wild rice. The data here provide a foundation for future work aimed at dissecting the genetic basis of disease resistance in rice, and the two wild rice lines will be useful germplasm for the molecular improvement of cultivated rice.

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Section: Introductionmentioning

confidence: 99%

Genome wide re-sequencing of newly developed Rice Lines from common wild rice (Oryza rufipogon Griff.) for the identification of NBS-LRR genes

Wen

Ghouri

et al. 2017

PLoS ONE

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“…However, new donors, especially from CWRs, are becoming increasingly important (Ahmad Ganie, Molla, Henry, Bhat, & Mondal, 2019; Solis et al., 2020). Several presumably beneficial QTL for salinity tolerance have been identified in rice at the seedling stage (Chen et al., 2020; L. Cheng et al., 2012; Jahan et al., 2020) and with beneficial alleles coming from CWRs (Tian, Tan, Liu, Cai, & Sun, 2011, Wang et al., 2017; Quan et al., 2018, Yichie, Brien, Berger, Roberts, & Atwell, 2018). These loci need to be genetically and physiologically characterized and their effects validated before molecular markers can be developed for more effective salinity screening and efficient development of salt‐tolerant varieties.…”

Section: Discussionmentioning

confidence: 99%

“…Since Pokkali and FL478 have been used as donor parents for salt tolerance in most breeding programs, there is a need to diversify the source of the trait. The introduction of new genotypes as donors, especially derived from CWRs, which might harbor novel beneficial alleles, is favorable (Z. Cheng et al., 2012; Liu et al., 2015; Shishido, Kikuchi, Nomura, & Ikehashi, 2006; Sun, Wang, Li, Yoshimura, & Iwata, 2001).…”

Section: Introductionmentioning

confidence: 99%

Phenotypic response of farmer‐selected CWR‐derived rice lines to salt stress in the Mekong Delta

et al. 2020

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Breeding for salt tolerance or abiotic stress, in general, requires rapid but reliable screening protocols that reflect the actual field situation as much as possible. A collection of 200 crop wild relative (CWR)-derived BC 3 F 3-4 rice (Oryza sativa L.) lines developed at the International Rice Research Institute (IRRI) were evaluated by farmers in the Mekong Delta over two seasons for agronomic performance. Fifty stable BC 3 F 5 lines were selected and subsequently screened in hydroponics using three NaCl concentrations to assess their phenotypic response to salt stress. The lines and check varieties were grown in a salinized Yoshida nutrient solution at three concentrations: 68, 102, and 13 mM NaCl. Several lines were identified to be tolerant to salinity stress and ANOVA showed significant differences among genotypes and NaCl concentrations. Root and shoot growth parameters showed an inverse relationship with increasing NaCl concentration. Population genetic analysis suggested four groups of genotypes, where the median salt injury score across the three NaCl concentrations was identified as the main clustering factor. Lines from Cluster 3 were identified as the most promising donors of salt tolerance.

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“…CWR is the close relative species of common cultivated rice (CCR, Oryza sativa L.) or Asian cultivated rice. Although many agronomic traits of CWR are inferior to those of CCR, the genetic polymorphism of CWR is richer than that of CCR [1][2][3][4]. Among CWR accessions there are some superior resources which possess excellent or specific agronomic traits like resistance to pest Open Access Full list of author information is available at the end of the article and disease, tolerance to abiotic stress, high yield quantitative trait locus/loci (QTL), etc.…”

Section: Introductionmentioning

confidence: 99%

Studies on the cold tolerance of ratoon ‘Chaling’ common wild rice

et al. 2020

Biol Res

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Background: Rice is the staple food of many people around the world. However, most rice varieties, especially widely grown indica varieties and hybrids, are sensitive to cold stress. In order to provide a basis for the utilization of a common wild rice (CWR, Oryza rufipogon Griff.) named 'Chaling' CWR in cold-tolerant rice breeding and deepen the understanding of rice cold tolerance, the cold tolerance of ratoon 'Chaling' CWR was studied under the stress of the natural low temperature in winter in Changsha, Hunan province, China, especially under the stress of abnormal natural low temperature in Changsha in 2008, taking other ratoon CWR accessions and ratoon cultivated rice phenotypes as control. Results:The results showed that ratoon 'Chaling' CWR can safely overwinter under the natural conditions in Changsha (28° 22′ N), Hunan province, China, which is a further and colder northern place than its habitat, even if it suffers a long-term low temperature stress with ice and snow. In 2008, an extremely cold winter appeared in Changsha, i.e., the average daily mean temperature of 22 consecutive days from January 13 to February 3 was − 1.0 °C, and the extreme low temperature was − 4.7 °C. After subjected to this long-term cold stress, the overwinter survival rate of ratoon 'Chaling' CWR was 100%, equals to that of ratoon 'Dongxiang' CWR which is northernmost distribution in the word among wild rice populations, higher than those of ratoon 'Fusui' CWR, ratoon ' Jiangyong' CWR, and ratoon 'Liujiang' CWR (63.55-83.5%) as well as those of ratoon 'Hainan' CWR, ratoon 'Hepu' CWR, and all the ratoon cultivated rice phenotypes including 3 japonica ones, 3 javanica ones, and 5 indica ones (0.0%). Conclusions:The results indicate that ratoon 'Chaling' CWR possesses strong cold tolerance and certain freezing tolerance.

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Genetic Diversity of Wild Rice Species in Yunnan Province of China

Cited by 9 publications

References 4 publications

Genome wide re-sequencing of newly developed Rice Lines from common wild rice (Oryza rufipogon Griff.) for the identification of NBS-LRR genes

Genome wide re-sequencing of newly developed Rice Lines from common wild rice (Oryza rufipogon Griff.) for the identification of NBS-LRR genes

Phenotypic response of farmer‐selected CWR‐derived rice lines to salt stress in the Mekong Delta

Studies on the cold tolerance of ratoon ‘Chaling’ common wild rice

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