Single-nucleotide polymorphism discovery by high-throughput sequencing in sorghum

Nelson, James C.; Wang, Shichen; Wu, Yuye; Li, Xianran; Antony, Ginny; White, Frank F.; Yu, Jianming

doi:10.1186/1471-2164-12-352

Cited by 88 publications

(74 citation statements)

References 49 publications

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“…The ratio of non-synonymous to synonymous SNP was 1.45 and 1.39 in Daewon and Hwangkeum, respectively (Table 4). This ratio is similar to ratio shown in soybean (1.40) which is higher than those in Arabidopsis, maize, and sorghum and rice (Clark et al, 2007;Hufford et al, 2012;Lam et al, 2010;McNally et al, 2009;Nelson et al, 2011).…”

Section: Discussionsupporting

confidence: 81%

Distribution of Genetic Variants in Korean Soybeans

Song¹,

Kim²,

Yoon³

et al. 2015

Korean J. Crop Sci.

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Next generation sequencing technologies provide opportunities to reveal the genetic variants and differentially expressedgenes. The genetic variants are closely relevance to understanding of genes and phenotypic differences related to agronomic characteristics among cultivars. In this study, we conducted RNA-seq using two Korean soybean accessions, including Daewon and Hwangkeum, by using next generation sequencing against Williams 82 genome as reference. A number of variants such assingle nucleotide variants (SNV), multiple nucleotide variants (MNV), insertion/deletion (InDel) and replacement, was 34,411 and 55,544 in Daewon and Hwangkeum, respectively. Among these variants, 9,611 nonsynonymous variants were detected within 4,290 genes in Daewon and 13,225 non-synonymous variants were located on 5,672 genes in Hwangkeum. The distribution of nonsynonymous variants and expression values of genes can serve as invaluable resource for genotyping and study of traits within genes for soybean improvements.

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Section: Discussionsupporting

confidence: 81%

Distribution of Genetic Variants in Korean Soybeans

Song¹,

Kim²,

Yoon³

et al. 2015

Korean J. Crop Sci.

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“…From this point of view, genotypingby-sequencing (GBS) technique offers many more opportunities. Discovery of a large number of SNPs using GBS was demonstrated in maize [45] and sorghum [46]. GBS not only increases the sequencing throughput by several orders of magnitude but also has multiplexing capabilities [47].…”

Section: Snp Discovery In Complex Plant Genomesmentioning

confidence: 99%

Maize (Zea mays L.) Genome Diversity as Revealed by RNA-Sequencing

2014

The Role of Bioinformatics in Agriculture

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The use of molecular markers has revolutionized the pace and precision of plant genetic analysis which in turn facilitated the implementation of molecular breeding of crops. The last three decades have seen tremendous advances in the evolution of marker systems and the respective detection platforms. Markers based on single nucleotide polymorphisms (SNPs) have rapidly gained the center stage of molecular genetics during the recent years due to their abundance in the genomes and their amenability for high-throughput detection formats and platforms. Computational approaches dominate SNP discovery methods due to the everincreasing sequence information in public databases; however, complex genomes pose special challenges in the identification of informative SNPs warranting alternative strategies in those crops. Many genotyping platforms and chemistries have become available making the use of SNPs even more attractive and efficient. This paper provides a review of historical and current efforts in the development, validation, and application of SNP markers in QTL/gene discovery and plant breeding by discussing key experimental strategies and cases exemplifying their impact.

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“…Arabidopsis, rice, sorghum, soybean, wheat, eucalyptus, potato, peach, cotton, oil rape (Ahmad et al, 2011;Allen et al, 2011;Barchi et al, 2011;Byers et al, 2012;Delourme et al, 2013;Hendre et al, 2012;Huang et al, 2010;Lai et al, 2015;Li et al, 2014;McNally et al, 2009;Nelson et al, 2011;Trebbi et al, 2011;Yamamoto et al, 2010).…”

Section: Numerous Studies Employ Next Generation Sequencing For Snp Dmentioning

confidence: 99%

Construction and analysis of the Brassica oleracea pangenome

Golicz¹

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This thesis describes the construction and analysis of a first Brassica oleracea pangenome. It also presents a pipeline that was developed and implemented in order to build and analyse the pangenome.B. oleracea is a species of high economic importance encompassing crops like broccoli, Brussels sprout, cabbage, cauliflower, kale and kohlrabi. Additionally, it is of high interest to the scientific community because the crops display remarkable morphological and physiological variation and the genetic underpinning of this variation is not fully understood.Recent years have seen an explosion of genome sequencing projects. It has also become clear that there is a significant amount of presence/absence and copy number variation between individuals of the same species, and a reference sequence from a single individual is unable to capture all of the genomic information necessary to fully characterize a species. The term pangenome was coined to describe all the genomic (genic) sequence information found within species.We have hypothesized that some of the phenotypic variation found in the B. oleracea crops might be due to presence/absence variants and therefore we have set out to construct and analyse the B. oleracea pangenome.The pipeline designed was composed of three main steps 1. Pangenome assembly using an iterative mapping and assembly approach and pangenome annotation. Chalhoub, B., Denoeud, F., Liu, S., Parkin, I.A.P., Tang, H., Wang, X., Chiquet, J., Belcram, H., Tong, C., Samans, B., Corréa, M., Da Silva, C., Just, J., Falentin, C., Koh, C.S., Le Clainche, I., Bernard, M., Bento, P., Noel, B., Labadie, K., Alberti, A., Charles, M., Arnaud, D., Guo, H., Daviaud, C., Alamery, S., Jabbari, K., Zhao, M., Edger, P.P., Chelaifa, H., Tack, D., Lassalle, G., Mestiri, I., Schnel, N., Le Paslier, M.-C., Fan, G., Renault, V., Bayer, P.E., Golicz, A.A., Manoli, S., Lee, T.-H., Thi, V.H.D., Chalabi, S., Hu, Q., Fan, C., Tollenaere, R., Lu, Y., Battail, C., Shen, J., Sidebottom, C.H.D., Wang, X., Canaguier, A., Chauveau, A., Bérard, A., Deniot, G., Guan, M., Liu, Z., Sun, F., Lim, Y.P., Lyons, E., Town, C.D., Bancroft, I., Wang, X., Meng, J., Ma, J., Pires, J.C., King, G.J., Brunel, D., Delourme, R., Renard, M.,

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Single-nucleotide polymorphism discovery by high-throughput sequencing in sorghum

Cited by 88 publications

References 49 publications

Distribution of Genetic Variants in Korean Soybeans

Distribution of Genetic Variants in Korean Soybeans

Maize (Zea mays L.) Genome Diversity as Revealed by RNA-Sequencing

Construction and analysis of the Brassica oleracea pangenome

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