Research Trends and Challenges of Using CRISPR/Cas9 for Improving Rice Productivity

Nowadays, rice production faces significant challenges due to population pressure, global climate change, and outbreak of various pests and diseases. Breeding techniques used to improve rice traits include mutant breeding, cross breeding, heterogeneity, transformation, molecular markers, genome-wide association study (GWAS), and so on. Since the recently developed CRISPR/Cas9 technology can directly target a specific part of a desired gene to induce mutation, it can be used as a powerful means to expand genetic diversity of crops and develop new varieties. So far, CRISPR/Cas9 technology has been used for improving rice characteristics such as high yield, good quality, abundant nutrition, pest and disease resistance, herbicide resistance, and biotic and abiotic stress resistance. This review highlights the mechanisms and optimization of the CRISPR system and its application to rice crop, including resistance to biotic and abiotic stresses, and improved rice quality and yield.

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Genome-Wide Association Study for Adaptation to Agronomic Plant Density: A Component of High Yield Potential in Spring Wheat

Crop Science ◽

10.2135/cropsci2015.03.0139 ◽

2015 ◽

Vol 55 (6) ◽

pp. 2609-2619 ◽

Cited By ~ 25

Author(s):

Sivakumar Sukumaran ◽

Matthew P. Reynolds ◽

Marta S. Lopes ◽

José Crossa

Keyword(s):

Association Study ◽

Spring Wheat ◽

Genome Wide Association Study ◽

Plant Density ◽

Genome Wide Association ◽

Yield Potential ◽

High Yield ◽

Genome Wide ◽

High Yield Potential

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Genome-Wide Association Study Reveals Marker–Trait Associations for Early Vegetative Stage Salinity Tolerance in Rice

Plants ◽

10.3390/plants10030559 ◽

2021 ◽

Vol 10 (3) ◽

pp. 559

Author(s):

Ashutosh Kumar Yadav ◽

Aruna Kumar ◽

Nitasha Grover ◽

Ranjith Kumar Ellur ◽

Haritha Bollinedi ◽

...

Keyword(s):

Salt Tolerance ◽

Association Study ◽

Salinity Tolerance ◽

Genome Wide Association Study ◽

Genomic Region ◽

Seedling Stage ◽

Genome Wide Association ◽

High Yield ◽

Genome Wide ◽

Trait Associations

Rice germplasm is a rich resource for discovering genes associated with salt tolerance. In the current study, a set of 96 accessions were evaluated for seedling stage salinity tolerance and its component traits. Significant phenotypic variation was observed among the genotypes for all the measured traits and eleven accessions with high level of salt tolerance at seedling stage were identified. The germplasm set comprised of three sub-populations and genome-wide association study (GWAS) identified a total of 23 marker–trait associations (MTAs) for traits studied. These MTAs were located on rice chromosomes 1, 2, 5, 6, 7, 9, and 12 and explained the trait phenotypic variances ranging from 13.98 to 29.88 %. Twenty-one MTAs identified in this study were located either in or near the previously reported quantitative trait loci (QTLs), while two MTAs namely, qSDW2.1 and qSNC5 were novel. A total of 18 and 13 putative annotated candidate genes were identified in a genomic region spanning ~200 kb around the MTAs qSDW2.1 and qSNC5, respectively. Some of the important genes underlying the novel MTAs were OsFBA1,OsFBL7, and mTERF which are known to be associated with salinity tolerance in crops. These MTAs pave way for combining salinity tolerance with high yield in rice genotypes through molecular breeding.

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Genome-Wide Association Study Reveals the QTLs for Seed Storability in World Rice Core Collections

Plants ◽

10.3390/plants10040812 ◽

2021 ◽

Vol 10 (4) ◽

pp. 812

Author(s):

Fangxi Wu ◽

Xi Luo ◽

Lingqiang Wang ◽

Yidong Wei ◽

Jianguo Li ◽

...

Keyword(s):

Association Study ◽

Genome Wide Association Study ◽

Rice Genome ◽

Genome Wide Association ◽

Rice Seed ◽

Core Collections ◽

Genome Wide ◽

A Genome ◽

New Varieties ◽

Seed Storability

Seed storability is a main agronomically important trait to assure storage safety of grain and seeds in rice. Although many quantitative trait loci (QTLs) and associated genes for rice seed storability have been identified, the detailed genetic mechanisms of seed storability remain unclear in rice. In this study, a genome-wide association study (GWAS) was performed in 456 diverse rice core collections from the 3K rice genome. We discovered the new nine QTLs designated as qSS1-1, qSS1-2, qSS2-1, qSS3-1, qSS5-1, qSS5-2, qSS7-1, qSS8-1, and qSS11-1. According to the analysis of the new nine QTLs, our results could well explain the reason why seed storability of indica subspecies was superior to japonica subspecies in rice. Among them, qSS1-2 and qSS8-1 were potentially co-localized with a known associated qSS1/OsGH3-2 and OsPIMT1, respectively. Our results also suggest that pyramiding breeding of superior alleles of these associated genes will lead to new varieties with improved seed storability in the future.

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An RTM-GWAS procedure reveals the QTL alleles and candidate genes for three yield-related traits in upland cotton

BMC Plant Biology ◽

10.1186/s12870-020-02613-y ◽

2020 ◽

Vol 20 (1) ◽

Author(s):

Junji Su ◽

Caixiang Wang ◽

Qi Ma ◽

Ai Zhang ◽

Chunhui Shi ◽

...

Keyword(s):

Candidate Genes ◽

Upland Cotton ◽

Genome Wide Association Study ◽

Linkage Disequilibrium Block ◽

High Yield ◽

Phenotypic Traits ◽

Potential Candidate ◽

Haplotype Allele ◽

Fiber Yield ◽

Genome Wide

Abstract Background Cotton (Gossypium spp.) fiber yield is one of the key target traits, and improved fiber yield has always been thought of as an important objective in the breeding programs and production. Although some studies had been reported for the understanding of genetic bases for cotton yield-related traits, the detected quantitative trait loci (QTL) for the traits is still very limited. To uncover the whole-genome QTL controlling three yield-related traits in upland cotton (Gossypium hirsutum L.), phenotypic traits were investigated under four planting environments and 9244 single-nucleotide polymorphism linkage disequilibrium block (SNPLDB) markers were developed in an association panel consisting of 315 accessions. Results A total of 53, 70 and 68 significant SNPLDB loci associated with boll number (BN), boll weight (BW) and lint percentage (LP), were respectively detected through a restricted two-stage multi-locus multi-allele genome-wide association study (RTM-GWAS) procedure in multiple environments. The haplotype/allele effects of the significant SNPLDB loci were estimated and the QTL-allele matrices were organized for offering the abbreviated genetic composition of the population. Among the significant SNPLDB loci, six of them were simultaneously identified in two or more single planting environments and were thought of as the stable SNPLDB loci. Additionally, a total of 115 genes were annotated in the nearby regions of the six stable SNPLDB loci, and 16 common potential candidate genes controlling target traits of them were predicted by two RNA-seq data. One of 16 genes (GH_D06G2161) was mainly expressed in the early ovule-development stages, and the stable SNPLDB locus (LDB_19_62926589) was mapped in its promoter region. Conclusion This study identified the QTL alleles and candidate genes that could provide important insights into the genetic basis of yield-related traits in upland cotton and might facilitate breeding cotton varieties with high yield.

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Genome-wide association mapping for resistance to leaf, stem, and yellow rusts of common wheat under field conditions of South Kazakhstan

PeerJ ◽

10.7717/peerj.9820 ◽

2020 ◽

Vol 8 ◽

pp. e9820

Author(s):

Yuliya Genievskaya ◽

Yerlan Turuspekov ◽

Aralbek Rsaliyev ◽

Saule Abugalieva

Keyword(s):

Common Wheat ◽

Genome Wide Association Study ◽

Phenotypic Diversity ◽

Field Conditions ◽

Genome Wide Association ◽

Yield Potential ◽

High Yield ◽

Genome Wide ◽

Wide Range ◽

Mixed Reaction

Common or bread wheat (Triticum aestivum L.) is the most important cereal crop in the world, including Kazakhstan, where it is a major agricultural commodity. Fungal pathogens producing leaf, stem, and yellow (stripe) rusts of wheat may cause yield losses of up to 50–60%. One of the most effective methods for preventing these losses is to develop resistant cultivars with high yield potential. This goal can be achieved using complex breeding studies, including the identification of key genetic factors controlling rust disease resistance. In this study, a panel consisting of 215 common wheat cultivars and breeding lines from Kazakhstan, Russia, Europe, USA, Canada, Mexico, and Australia, with a wide range of resistance to leaf rust (LR), stem rust (SR), and yellow rust (YR) diseases, was analyzed under field conditions in Southern Kazakhstan. The collection was genotyped using the 20K Illumina iSelect DNA array, where 11,510 informative single-nucleotide polymorphism markers were selected for further genome-wide association study (GWAS). Evaluation of the phenotypic diversity over 2 years showed a mostly mixed reaction to LR, mixed reaction/moderate susceptibility to SR, and moderate resistance to YR among wheat accessions from Kazakhstan. GWAS revealed 45 marker–trait associations (MTAs), including 23 for LR, 14 for SR, and eight for YR resistances. Three MTAs for LR resistance and one for SR resistance appeared to be novel. The MTAs identified in this work can be used for marker-assisted selection of common wheat in Kazakhstan in breeding new cultivars resistant to LR, SR, and YR diseases. These findings can be helpful for pyramiding genes with favorable alleles in promising cultivars and lines.

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Combination of favorable gene haplotypes plays an important role in rice hybrid grain quality traits based on genome-wide association analysis

10.1101/2020.06.04.134023 ◽

2020 ◽

Author(s):

Lanzhi Li ◽

Xingfei Zheng ◽

Xueli Zhang ◽

Kai Xu ◽

Shufeng Song ◽

...

Keyword(s):

Grain Quality ◽

Genome Wide Association Study ◽

Amylose Content ◽

Genome Wide Association ◽

High Yield ◽

Quality Trait ◽

Rice Grain ◽

Quality Traits ◽

Genome Wide ◽

A Genome

SummaryYield level and grain quality determine the commercial potential of rice (Oryza sativa L.) varieties. Mining and using genes that control important rice grain quality characteristics are major tasks for plant breeders. Here, a genome-wide association study was conducted to determine the genetic bases of 12 rice grain quality traits in 113 varieties and 565 testcross hybrids. A total of 56 significant SNPs were associated with 9 of the traits in variety phenotypic, general combining ability, testcross hybrid phenotypic and mid-parental heterotic datasets, from which 45 novel loci were identified. The cumulative effects of superior alleles or favorable haplotypes of genes closest to significant quality trait-associated loci were found in the four datasets. Additionally, the favorable gene haplotypes performed better than those of superior alleles in the variety and testcross hybrid datasets. Pyramiding the favorable haplotypes of five cloned rice grain quality genes resulted in a very low amylose content and high yield in the latter. These testcross hybrids had rice grain qualities similar to their parental lines but with much higher yields. The amylose content, grain width and grain length predictions for potential hybrids among the 113 varieties using genomic selection based on the BayesB method revealed a performance trend similar to those the testcross hybrids in our study. Thus, the selection of combination of favorable rice quality-related gene haplotypes is recommended to breed hybrids with high yields and elite grain qualities.

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Innovative Strategies to Develop Abiotic and Biotic Stress Tolerance in Mustard (Brassicaceae)

10.5772/intechopen.95973 ◽

2021 ◽

Author(s):

Bahaderjeet Singh ◽

Amanpreet Singh Sran ◽

Gagandeep Singh Sohi

Keyword(s):

Stress Tolerance ◽

Biotic Stress ◽

Abiotic Stress Tolerance ◽

High Yield ◽

Biotic And Abiotic Stress ◽

Innovative Strategies ◽

Brassica Crop ◽

Mustard Crop ◽

Breeding Techniques

Mustard crop is the third important source of vegetable oil randomly below soybean L. and palm, all over the world. Brassica crop is extremely susceptible to some biotic and abiotic stresses and they significantly influence the quality and quantity of the crop. In the past generally breeding techniques are used to develop resistance in mustard to avoid diseases though various pathogens are soon able to overcome that resistance by modifying their metabolic cycles. To bear the challenge there is an urgent need to develop abiotic as well as biotic stress tolerant plants using advanced techniques by understanding metabolic and biochemical pathways of plants and pathogens. Several techniques such selection of stress tolerance microbes, metabolite, enzymes, and genes are very important to avoid stresses. Whereas several techniques such as deployment of molecular markers for breeding, identification of Quantitative trait loci (QTL), in vitro tissue culture etc. can be more useful to improve biotic and abiotic stress tolerance in mustard. To develop healthy and high yield varieties, the mix of these techniques is needs to be implemented.

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