QTG-Seq Accelerates QTL Fine Mapping through QTL Partitioning and Whole-Genome Sequencing of Bulked Segregant Samples

Zhang, Hongwei; Wang, Xi; Pan, Qingchun; Li, Pei; Liu, Yun-Jun; Lu, Xiaoduo; Zhong, Wanshun; Li, Minqi; Han, Linqian; Li, Juan; Wang, Pingxi; Li, Dongdong; Liu, Yan; Li, Qing; Yang, Fang; Zhang, Yuanming; Wang, Guoying; Lin, Li

doi:10.1016/j.molp.2018.12.018

Cited by 81 publications

(74 citation statements)

References 55 publications

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“…The third question is how to rapidly clone candidate genes from the large number of QTLs. One solution is to combine genetic transformation technology, CRISPR/Cas9 technology, other omics data and statistical methods for speeding up QTL cloning (e.g., QTG-seq; Zhang et al, 2019a). This information could be used in omics-based strategies as well as in systemic and synthetic biology in molecular design breeding or molecular module programs and will greatly facilitate future agronomic improvements (Figure 2A) (Li et al, 2018;Wing et al, 2018;Zhang et al, 2019b).…”

Section: High-throughput Phenotyping and Genetic Mappingmentioning

confidence: 99%

“…Next-generation sequencing technology has greatly accelerated progress in functional genomics (Huang et al, 2010;Werner, 2010;Li et al, 2018), allowing quantitative trait locus (QTL) mapping and genome-wide association studies (GWASs) (Xiao et al, 2017) to become powerful tools for elucidating the genetic architecture of complex traits (Atwell et al, 2010;Huang et al, 2010;Tian et al, 2011;Wang et al, 2018a;Zhang et al, 2019a), and many genes governing important agronomic traits have been identified (Zuo and Li, 2014;Yao et al, 2018;Fernie and Yan, 2019;Shi et al, 2019). For example, before 2000, only approximately 130 genes had been cloned in rice.…”

Section: Introductionmentioning

confidence: 99%

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Crop Phenomics and High-Throughput Phenotyping: Past Decades, Current Challenges, and Future Perspectives

et al. 2020

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Since whole-genome sequencing of many crops has been achieved, crop functional genomics studies have stepped into the big-data and high-throughput era. However, acquisition of large-scale phenotypic data has become one of the major bottlenecks hindering crop breeding and functional genomics studies. Nevertheless, recent technological advances provide us potential solutions to relieve this bottleneck and to explore advanced methods for large-scale phenotyping data acquisition and processing in the coming years. In this article, we review the major progress on high-throughput phenotyping in controlled environments and field conditions as well as its use for post-harvest yield and quality assessment in the past decades. We then discuss the latest multi-omics research combining high-throughput phenotyping with genetic studies. Finally, we propose some conceptual challenges and provide our perspectives on how to bridge the phenotype-genotype gap. It is no doubt that accurate high-throughput phenotyping will accelerate plant genetic improvements and promote the next green revolution in crop breeding.

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Section: High-throughput Phenotyping and Genetic Mappingmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Crop Phenomics and High-Throughput Phenotyping: Past Decades, Current Challenges, and Future Perspectives

et al. 2020

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“…Similarly, QTL-Seq approach was applied to fine-map bacterial wilt resistance genes and develop diagnostic markers for use in breeding in the case of groundnut (Luo et al 2019a). Adoption of QTL-Seq is increasingly reported for delineating candidate QTLs for both qualitative and quantitative traits (Yang et al 2017;Li et al 2018;Zhang et al 2018;Clevenger et al 2018;Zhang et al 2019;Luo et al 2019b).…”

Section: Role Of Ngs In Accelerating High-resolution Mapping and Genementioning

confidence: 99%

Fine mapping and gene cloning in the post-NGS era: advances and prospects

et al. 2020

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Improvement in traits of agronomic importance is the top breeding priority of crop improvement programs. Majority of these agronomic traits show complex quantitative inheritance. Identification of quantitative trait loci (QTLs) followed by fine mapping QTLs and cloning of candidate genes/QTLs is central to trait analysis. Advances in genomic technologies revolutionized our understanding of genetics of complex traits, and genomic regions associated with traits were employed in marker-assisted breeding or cloning of QTLs/genes. Next-generation sequencing (NGS) technologies have enabled genomewide methodologies for the development of ultra-high-density genetic linkage maps in different crops, thus allowing placement of candidate loci within few kbs in genomes. In this review, we compare the marker systems used for fine mapping and QTL cloning in the pre-and post-NGS era. We then discuss how different NGS platforms in combination with advanced experimental designs have improved trait analysis and fine mapping. We opine that efficient genotyping/sequencing assays may circumvent the need for cumbersome procedures that were earlier used for fine mapping. A deeper understanding of the trait architectures of agricultural significance will be crucial to accelerate crop improvement.

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“…Also, statistical methods for the association of phenotypic and genotypic data are used for linkage mapping and GWAS. Other methods that only use extreme plant materials for gene mapping (such as MutMap [120] , BAR-Seq [121] , QTL-Seq [122] , QTG-Seq [123] and XP-GWAS [124] ) have proved beneficial in genetic research on quality and quantitative traits. Moreover, bulked segregant analysis of genomes, metabolomes, and proteomes has great potential for genetic mapping, plant breeding, and molecular marker development [125] .…”

Section: Molecular Breeding For High Pue In Maizementioning

confidence: 99%

Genetic study and molecular breeding for high phosphorus use efficiency in maize

Li¹,

Meng²,

Kuang³

et al. 2019

Front. Agr. Sci. Eng.

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Phosphorus is the second most important macronutrient after nitrogen and it has many vital functions in the life of plants. Most soils have a low available P content, which has become a key limiting factor for increasing crop production. Also, low P use efficiency (PUE) of crops in conjunction with excessive application of P fertilizers has resulted in serious environmental problems. Thus, dissecting the genetic architecture of crop PUE, mining related quantitative trait loci (QTL) and using molecular breeding methods to improve high PUE germplasm are of great significance and serve as an efficient approach for the development of sustainable agriculture. In this review, molecular and phenotypic characteristics of maize inbred lines with high PUE, related QTL and genes as well as low-P responses are summarized. Based on this, a breeding strategy applying genomic selection as the core, and integrating the existing genetic information and molecular breeding techniques is proposed for breeding high PUE maize inbred lines and hybrids.

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QTG-Seq Accelerates QTL Fine Mapping through QTL Partitioning and Whole-Genome Sequencing of Bulked Segregant Samples

Cited by 81 publications

References 55 publications

Crop Phenomics and High-Throughput Phenotyping: Past Decades, Current Challenges, and Future Perspectives

Crop Phenomics and High-Throughput Phenotyping: Past Decades, Current Challenges, and Future Perspectives

Fine mapping and gene cloning in the post-NGS era: advances and prospects

Genetic study and molecular breeding for high phosphorus use efficiency in maize

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