Rapid Identification of Major QTLs Associated with Rice Grain Weight and Their Utilization

Xu, Feifei; Sun, Xiao; Chen, Yaling; Huang, Yan; Tong, Chuan; Bao, Jinsong

doi:10.1371/journal.pone.0122206

Cited by 59 publications

(54 citation statements)

References 34 publications

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“…This version has several attractive features: (1) no requirement of the reference genome sequences, (2) pre-designed RRL schemes avoiding large set of repetitive sequences, (3) double barcode system couple with NGS technique amenable for high-throughput and accurate SNP detection in large populations, and (4) cost-effective for researchers. Application of SLAF-seq for de novo SNP discovery, genotyping and mapping has been demonstrated in a variety of plant species including rice (Oryza Sativa L.) (Xu et al, 2015), soybean (Glycine max (L.) Merr.) , mei (Prunus mume Sieb.…”

Section: Introductionmentioning

confidence: 99%

Detection of SNPs based on DNA specific-locus amplified fragment sequencing in Chinese fir (Cunninghamia lanceolata (Lamb.) Hook)

Shu

Zheng

2016

Dendrobiology

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Compared to angiosperms, conifers represent more complex genomes with larger giga-genome size. To detect large-scale single nucleotide polymorphisms (SNPs), whole genome sequencing of a conifer population is still unaffordable. In this work, we report the use of DNA specific-locus amplified fragment sequencing (SLAF-seq) for large-scale SNP detection in Chinese fir (Cunninghamia lanceolata (Lamb.) Hook), an ecological and economic important conifer in China. SLAF libraries of 18 parent clones of a Chinese fir 2.5 generation seed orchard were sequenced and a total of 117,924 SLAFs were developed. We detected 147,376 SNPs from these SLAFs; 146,231 of them represented simple nucleotide change in A/G, C/T, A/C, A/T, C/G or G/T. The most frequent SNPs occurred in C/T (34.3%), while the majority of SNPs (68.2%) belonged to transition events (A/G and C/T). Notably, all the sequenced samples had high portion (78.2-80.9%) of common SNPs indicating that the Chinese fir genomes tended to change its nucleotides at common loci. 48,406 informative SNPs were then successfully utilized to genotype the tested samples (n = 18) followed by a phylogenetic tree to clarify their genetic relationship. Furthermore, a set of very high linkage disequilibrium (0.51-1.00) were identified from these informative SNPs. In brief, our work demonstrated that SLAF-seq is an alternative and cost-effectively high-throughput approach for large-scale SNP exploitation in Chinese fir. While the obtained SNPs offer useful marker resource for further genetic and genomic studies and will be helpful for Chinese fir breeding programs.

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Section: Introductionmentioning

confidence: 99%

Detection of SNPs based on DNA specific-locus amplified fragment sequencing in Chinese fir (Cunninghamia lanceolata (Lamb.) Hook)

Shu

Zheng

2016

Dendrobiology

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“…The other three QTLs for TGW, qTGW3.1, qTGW3.2 and qTGW3.3, corresponded to GS3 (Fan et al 2006), qGL3 (Zhang et al 2012) and qTGW3.2 (Tang et al 2013), respectively, and were detected previously (Xu et al 2015b). GS3 is a major QTL for grain length and grain weight and a minor QTL for grain width (Fan et al 2006).…”

Section: Qtls For Grain Shape and Grain Weight Traitsmentioning

confidence: 67%

“…The numbers of QTLs for TGW, GL, GW and GLW were 5, 5, 4 and 5, respectively. Among them, nine QTLs on chromosome 3 were reported previously (Xu et al 2015b), while the remaining ten QTLs were located on chromosome 2, 4 and 5. Owing to the use of different linkage maps, the LOD score and PVE relatively changed between the previous study based on only chromosome 3 (Xu et al 2015b) and the present study based on the whole genome of rice (Table 3).…”

Section: Qtls For Grain Shape and Grain Weight Traitsmentioning

confidence: 97%

“…Additionally, and FLO2 regulates grain size and starch quality by affecting storage substance accumulation in the endosperm (She et al 2010). Moreover, a number of QTLs have been finely mapped in different populations, such as qGL7, qSS7, qTGW1.1, qTGW3.2 and tgw11 (Bai et al 2010;Oh et al 2011;Qiu et al 2012;Tang et al 2013;Xu et al 2015b;Zhang et al 2015). Association mapping that deals with diverse rice varieties is of great importance in detecting QTLs for agronomic traits (Xu et al 2014;Huang et al 2010Huang et al , 2012.…”

Section: Introductionmentioning

confidence: 99%

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Identification of QTLs for agronomic traits in indica rice using an RIL population

Huang

Bao

2015

Genes Genom

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Increasing grain weight and breeding for ideal plant architecture are two means to improve the productivity of rice. Quantitative trait locus (QTL) mapping was conducted on ten yield component traits using a recombinant inbred line population derived from an indica 9 indica cross (M201 9 JY293). Correlation analysis revealed that plant height, panicle length and flag leaf length, classified as plant morphology traits, were positively correlated with grain shape traits such as thousandgrain weight, grain length and grain width. Two tillering traits, total and effective tiller numbers, showed negative correlations with nearly all the other traits tested. A total of 37 QTLs were detected over the 2-year study period, and 14 of them were identified in both years. Four clustered QTLs corresponding to known genes/QTLs (GW2, GS3, qGL3 and qTGW3.3) were revealed on chromosomes 2 and 3, which had pleiotropic effects on grain weight and plant architecture traits. QTL mapping demonstrated that qGL3 was a major QTL controlling grain length and weight, as well as plant height, panicle length and flag leaf length in rice. Three new QTLs, qTGW3.0, qGL2.2 and qETN4, were detected in both years and worth attention in breeding for high-yield rice varieties.

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“…Variants of NGS-based QTL identification methods, such as X-QTL, MutMap, QTL-seq, SHOREmap, and NGM, have been reviewed elsewhere [99]. Among the various NGS-based QTL mapping approaches, QTL-seq, the whole genome re-sequencing-based mapping of QTL [100], can successfully be applied to dissect key quantitative traits underlying biotic and abiotic stresses in major African staple food crops such as cassava, yam, tef, and legumes.…”

Section: Qtl Identificationmentioning

confidence: 99%

Perspectives on the Application of Next-generation Sequencing to the Improvement of Africa’s Staple Food Crops

Gedil¹,

Ferguson²,

Girma³

et al. 2016

Next Generation Sequencing - Advances, Applications and Challenges

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The persistent challenge of insufficient food, unbalanced nutrition, and deteriorating natural resources in the most vulnerable nations, characterized by fast population growth, calls for utilization of innovative technologies to curb constraints of crop production. Enhancing genetic gain by using a multipronged approach that combines conventional and genomic technologies for the development of stress-tolerant varieties with high yield and nutritional quality is necessary. The advent of nextgeneration sequencing (NGS) technologies holds the potential to dramatically impact the crop improvement process. NGS enables whole-genome sequencing (WGS) and re-sequencing, transcriptome sequencing, metagenomics, as well as high-throughput genotyping, which can be applied for genome selection (GS). It can also be applied to diversity analysis, genetic and epigenetic characterization of germplasm and pathogen detection, identification, and elimination. High-throughput phenotyping, integrated data management, and decision support tools form the necessary supporting environment for effective utilization of genome sequence information. It is important that these opportunities for mainstreaming innovative breeding strategies, enabled by cutting-edge "Omics" technologies, are seized in Africa; however, several constraints must be addressed before the benefit of NGS can be fully realized. African breeding programs must have access to high-throughput genotyping facilities, capacity in the application of genome selection and marker-assisted breeding must be built and supported by capacity in genomic analysis and bioinformatics. This chapter demonstrates how interventions with NGS-enabled innovative strategies can be applied to increase genetic gain with insights from the Consortium of International

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Rapid Identification of Major QTLs Associated with Rice Grain Weight and Their Utilization

Cited by 59 publications

References 34 publications

Detection of SNPs based on DNA specific-locus amplified fragment sequencing in Chinese fir (Cunninghamia lanceolata (Lamb.) Hook)

Detection of SNPs based on DNA specific-locus amplified fragment sequencing in Chinese fir (Cunninghamia lanceolata (Lamb.) Hook)

Identification of QTLs for agronomic traits in indica rice using an RIL population

Perspectives on the Application of Next-generation Sequencing to the Improvement of Africa’s Staple Food Crops

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