Genome‐Wide Responses to Selection and Genetic Networks Underlying Submergence Tolerance in Rice

Wang, Wensheng; Fu, Binying; Ali, Jauhar; Xu, Jianlong; Gao, Yongming; Zheng, Tianqing; Zhang, Fan; Li, Zhikang

doi:10.3835/plantgenome2014.10.0066

Cited by 11 publications

(29 citation statements)

References 40 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Thus, this study presents another case in our efforts for simultaneous improvement and genetic dissection of complex traits by marker-facilitated characterization of donor introgression in selected ILs. Moreover, when compared with the previous reports [ 3 , 25 , 29 ], the inclusion of random populations in this study provided additional evidence to justify the strategy of selective introgression. Several interesting findings regarding the real power of this strategy and the genetic basis of CT at the reproductive stage in rice worth more discussion.…”

Section: Discussionsupporting

confidence: 49%

“…In this method, we used the minimum threshold of P<0.05 because of the small population sizes of the random populations. The third methodology was more comprehensive and was used to detect QTL and QTL networks in three steps based on the molecular quantitative genetics theory [ 3 , 29 ]. In this theory, two concepts, functional genetic units (FGUs) and the principle of hierarchy, are defined here based on two commonest types of functional relationships between genes acting in the same signaling pathways affecting complex traits.…”

Section: Methodsmentioning

confidence: 99%

“…To reveal the multi-locus structure of the detected FGUs–the putative genetic network underlying ST in the ILs from each BC population, pairwise gametic LD analyses were performed to characterize the relationships between alleles at all ST FGUs detected in ILs from each BC population [ 3 , 29 ]. The LD statistics [ 26 ], , were calculated using the genotypic data of ILs from each BC population, where , and were the frequencies of co-introgressed functional genotype AB, and functional genotypes at FGUs A and B, respectively.…”

Section: Methodsmentioning

confidence: 99%

See 2 more Smart Citations

QTL and QTL networks for cold tolerance at the reproductive stage detected using selective introgression in rice

et al. 2018

Self Cite

View full text Add to dashboard Cite

Low temperature stress is one of the major abiotic stresses limiting the productivity of Geng (japonica) rice grown the temperate regions as well as in tropical high lands worldwide. To develop rice varieties with improved cold tolerance (CT) at the reproductive stage, 84 BC2 CT introgression lines (ILs) were developed from five populations through backcross breeding. These CT ILs plus 310 random ILs from the same BC populations were used for dissecting genetic networks underlying CT in rice by detecting QTLs and functional genetic units (FGUs) contributing to CT. Seventeen major QTLs for CT were identified using five selective introgression populations and the method of segregation distortion. Of them, three QTLs were confirmed using the random populations and seven others locate in the regions with previously reported CT QTLs/genes. Using multi-locus probability tests and linkage disequilibrium (LD) analyses, 46 functional genetic units (FGUs) (37 single loci and 9 association groups or AGs) distributed in 37 bins (~20%) across the rice genome for CT were detected. Together, each of the CT loci (bins) was detected in 1.7 populations, including 18 loci detected in two or more populations. Putative genetic networks (multi-locus structures) underlying CT were constructed based on strong non-random associations between or among donor alleles at the unlinked CT loci/FGUs identified in the CT ILs, suggesting the presence of strong epistasis among the detected CT loci. Our results demonstrated the power and usefulness of using selective introgression for simultaneous improvement and genetic dissection of complex traits such as CT in rice.

show abstract

Section: Discussionsupporting

confidence: 49%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

QTL and QTL networks for cold tolerance at the reproductive stage detected using selective introgression in rice

et al. 2018

Self Cite

View full text Add to dashboard Cite

show abstract

“…With the rapid advancement of DNA-sequencing and multi-omics technology, whole-genome analyses of gene variations and genome diversity of different types of rice germplasm resources have become an essential part of rice germplasm characterization and utilization. These abundant rice germplasm resources provide sufficient materials for further dissecting the genetic basis of complex traits, identifying novel genes and their functions for future rice molecular breeding by design (Xie et al 2015;Wang et al 2015bWang et al , 2018a.…”

Section: Genomic Breeding For Gsrmentioning

confidence: 99%

Genomic Breeding of Green Super Rice Varieties and Their Deployment in Asia and Africa

Ali

Zhang

et al. 2020

Theor Appl Genet

Self Cite

View full text Add to dashboard Cite

Key message The "Green Super Rice" (GSR) project aims to fundamentally transform crop production techniques and promote the development of green agriculture based on functional genomics and breeding of GSR varieties by whole-genome breeding platforms. Abstract Rice (Oryza sativa L.) is one of the leading food crops of the world, and the safe production of rice plays a central role in ensuring food security. However, the conflicts between rice production and environmental resources are becoming increasingly acute. For this reason, scientists in China have proposed the concept of Green Super Rice for promoting resource-saving and environment-friendly rice production, while still achieving a yield increase and quality improvement. GSR is becoming one of the major goals for agricultural research and crop improvement worldwide, which aims to mine and use vital genes associated with superior agronomic traits such as high yield, good quality, nutrient efficiency, and resistance against insects and stresses; establish genomic breeding platforms to breed and apply GSR; and set up resource-saving and environment-friendly cultivation management systems. GSR has been introduced into eight African and eight Asian countries and has contributed significantly to rice cultivation and food security in these countries. This article mainly describes the GSR concept and recent research progress, as well as the significant achievements in GSR breeding and its application.

show abstract

“…Two strategies were adopted for detecting QTL associated with DT and LNT in this study. The first one was the approach of selective introgression ( Zhang et al, 2014 ; Wang et al, 2015 ). Of 63, 68, and 75 ILs from crosses HHZ × Teqing, HHZ × CDR22, and HHZ × OM1723, 18, 18, 21 ILs were selected once or twice for improved yield under severe drought ( Ali et al, 2017 ).…”

Section: Methodsmentioning

confidence: 99%

Genetic Dissection and Simultaneous Improvement of Drought and Low Nitrogen Tolerances by Designed QTL Pyramiding in Rice

et al. 2018

Self Cite

View full text Add to dashboard Cite

Drought and low nitrogen are the most common abiotic stresses limiting rice productivity in the rainfed rice areas of Asia and Africa. Development and adoption of green super rice (GSR) varieties with greatly improved drought tolerance (DT) and low nitrogen tolerance (LNT) are the most efficient way to resolve this problem. In this study, using three sets of trait-specific introgression lines (ILs) in a Xian (indica) variety Huanghuazhan (HHZ) background, we identified nine DT-QTL and seven LNT-QTL by a segregation distortion approach and a genome-wide association study, respectively. Based on performances of DT and LNT and genotypes at the detected QTL, two ILs M79 and M387 with DT and LNT were selected for cross-making to validate the identified QTL and to develop DT and LNT rice lines by pyramiding two DT-QTL (qDT3.9 and qDT6.3) and two LNT-QTL (qGY1 and qSF8). Using four pairs of kompetitive allele specific PCR (KASP) SNP markers, we selected 66 F2 individuals with different combinations of the target DT- and LNT-QTL favorable alleles and they showed expected improvement in DT and/or LNT, which were further validated by the significant improvement in DT and/or LNT of their F3 progeny testing. Based on evaluation of pyramiding lines in F3 lines under drought, low nitrogen (LN) and normal conditions, four promising pyramiding lines having different QTL favorable alleles were selected, which showed significantly improved tolerances to drought and/or LN than HHZ and their IL parents. Our results demonstrated that trait-specific ILs could effectively connect QTL mapping and QTL pyramiding breeding, and designed QTL pyramiding (DQP) using ILs could be more effective in molecular rice breeding for complex quantitative traits.

show abstract

Genome‐Wide Responses to Selection and Genetic Networks Underlying Submergence Tolerance in Rice

Cited by 11 publications

References 40 publications

QTL and QTL networks for cold tolerance at the reproductive stage detected using selective introgression in rice

QTL and QTL networks for cold tolerance at the reproductive stage detected using selective introgression in rice

Genomic Breeding of Green Super Rice Varieties and Their Deployment in Asia and Africa

Genetic Dissection and Simultaneous Improvement of Drought and Low Nitrogen Tolerances by Designed QTL Pyramiding in Rice

Contact Info

Product

Resources

About