Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean

Zhou, Zhengkui; Jiang, Yu; Wang, Zheng; Gou, Zhiheng; Lyu, Jun; Li, Weiyu; Yu, Yong; Shu, Liping; Zhao, Yingjun; Ma, Yanming; Fang, Chao; Shen, Yanting; Liu, Tengfei; Li, Congcong; Li, Qing; Wu, Mian; Wang, Min; Wu, Yunshuai; Dong, Yang; Wan, Wenting; Wang, Xiao; Ding, Zijing; Gao, Yue‐Dong; Xiang, Hui; Bao-cheng, Zhu; Lee, Suk-Ha; Wang, Wen; Tian, Zhixi

doi:10.1038/nbt.3096

Cited by 938 publications

(1,096 citation statements)

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“…In addition, genome-wide single nucleotide polymorphisms (SNPs) were also used to identify significant marker trait associations for economically important traits (Zhou et al, 2015a;Varshney et al, 2017). Resequencing germplasm lines also enabled us to understand the spatial and temporal trends in diversity in released varieties of chickpea (Thudi et al, 2016a), cultivated and wild accessions of soybean (Lam et al, 2010;Zhou et al, 2015a), and a reference set of pigeonpea Table 1). Resequencing of 28 Brazilian soybean cultivars suggested that, despite the diversification of modern Brazilian cultivars, the soybean germplasm remains very narrow because of the large number of genome regions that exhibit low diversity (Maldonado dos Santos et al, 2016).…”

Section: Sequencing and Genotypingmentioning

confidence: 99%

“…Several million structural variations that aid in trait mapping and trait improvement were reported (Kumar et al, 2016;Thudi et al, 2016b). In addition, genome-wide single nucleotide polymorphisms (SNPs) were also used to identify significant marker trait associations for economically important traits (Zhou et al, 2015a;Varshney et al, 2017). Resequencing germplasm lines also enabled us to understand the spatial and temporal trends in diversity in released varieties of chickpea (Thudi et al, 2016a), cultivated and wild accessions of soybean (Lam et al, 2010;Zhou et al, 2015a), and a reference set of pigeonpea Table 1).…”

Section: Sequencing and Genotypingmentioning

confidence: 99%

“…Genome wide SNPs based on resequencing of several germplasm lines were also used to identify marker-trait associations in the cases of legumes such as pigeonpea and soybean (Zhou et al, 2015a).…”

Section: Genomics-assisted Breedingmentioning

confidence: 99%

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Accelerating genetic gains in legumes for the development of prosperous smallholder agriculture: integrating genomics, phenotyping, systems modelling and agronomy

Varshney

Thudi

Pandey

et al. 2018

Journal of Experimental Botany

102

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Grain legumes form an important component of the human diet, provide feed for livestock, and replenish soil fertility through biological nitrogen fixation. Globally, the demand for food legumes is increasing as they complement cereals in protein requirements and possess a high percentage of digestible protein. Climate change has enhanced the frequency and intensity of drought stress, posing serious production constraints, especially in rainfed regions where most legumes are produced. Genetic improvement of legumes, like other crops, is mostly based on pedigree and performance-based selection over the past half century. To achieve faster genetic gains in legumes in rainfed conditions, this review proposes the integration of modern genomics approaches, high throughput phenomics, and simulation modelling in support of crop improvement that leads to improved varieties that perform with appropriate agronomy. Selection intensity, generation interval, and improved operational efficiencies in breeding are expected to further enhance the genetic gain in experimental plots. Improved seed access to farmers, combined with appropriate agronomic packages in farmers' fields, will deliver higher genetic gains. Enhanced genetic gains, including not only productivity but also nutritional and market traits, will increase the profitability of farming and the availability of affordable nutritious food especially in developing countries.

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Section: Sequencing and Genotypingmentioning

confidence: 99%

Section: Sequencing and Genotypingmentioning

confidence: 99%

See 1 more Smart Citation

Accelerating genetic gains in legumes for the development of prosperous smallholder agriculture: integrating genomics, phenotyping, systems modelling and agronomy

Varshney

Thudi

Pandey

et al. 2018

Journal of Experimental Botany

102

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show abstract

“…For instance, a comprehensive map of rice genome variation detected 55 selective sweeps-targeted genomic regions that have occurred during domestication by genome resequencing of diverse 1083 cultivated indica and japonica varieties and 446 accessions of wild rice species (O. rufipogon) 54 . In soybean, 302 wild and cultivated accessions have been resequenced leading to the identification of genes underlying domestication and improvement traits (including oil content, plant height, seed-coat colour and pubescence form) at a genome-wide scale 55 . In cucumber, the resequencing of 115 accessions has uncovered 112 domestication sweep regions containing a gene responsible for loss of bitterness in this vegetable crop 56 .…”

Section: Comparative and Phylogenetics Prospects Of Decoded Crop Planmentioning

confidence: 99%

Revisiting the Decoded Genomes to Promptly Reveal their Genomic Perspectives

et al. 2017

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Post Arabidopsis thaliana, 55 genomes comprising 49 different plant species have been decoded by use of clone-by-clone, whole genome shotgun and nextgeneration sequencing approaches. The structural outcomes of these sequenced genomes shed light on their genomic constitution, particularly the way genes, transposable elements and genetic markers are organized within the genomes. The functional outcomes provide a brief account of specific phenotypic trait characteristics of crop genomes by digging deep into the genetic make-up of transcription factors, regulatory elements and gene families governing multiple agronomic traits in these crop plants. The comparative and evolutionary outcomes deduce the genetic basis of biological diversity and basic process of genome evolution by analysing the syntenic relationships among genes and genomes/chromosomes of the sequenced crop plants. Therefore, a revisit to published genome sequence landmarks in 30 major cultivated food crops constituting major groups (cereals, legumes, vegetables, fruits, oilseeds and fibres) would significantly assist us to gain a detailed insight into their genome organization and dissect the structural, functional, comparative and evolutionary intricacies for identifying species-and lineage-specific genes controlling multiple characteristics in crop plants. The essential inputs obtained will be helpful in devising efficient strategies to develop high-yielding climateready crop varieties through translational genomics.

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“…To probe how soybean subpopulations have adapted to different geographic areas, and to identify the genes responsible for domestication traits, Zhou et al performed a large-scale assessment of soybean domestication and improvement by re-sequencing 302 wild, landrace, and improved soybean accessions at >11× depth [7]. The large dataset produced approximately two-fold more SNPs and small indels than those previously reported.…”

mentioning

confidence: 99%