Domestication footprints anchor genomic regions of agronomic importance in soybeans

Han, Yingpeng; Zhao, Xue; Liu, Dongyuan; Li, Yinghui; Lightfoot, David A.; Yang, Zhijiang; Zhao, Lin; Zhou, Gang; Wang, Zhikun; Huang, Long; Zhang, Zhiwu; Qiu, Lijuan; Zheng, Hongkun; Li, Wenbin

doi:10.1111/nph.13626

Cited by 132 publications

(122 citation statements)

References 46 publications

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“…et Zucc) can be found from Southern China as well as throughout East Asia, and as far north as the Russian Far East (latitudes 24 o to 53 o North). Domesticated soybean has a historical range that extends north and south from central China possibly centered at the Huang-Huai Valley [27]. Wild soybeans expanding into a wide range of latitudes while maintaining photoperiod sensitivity implies strong natural selection for variant alleles of maturity genes.…”

Section: Discussionmentioning

confidence: 99%

The development and use of a molecular model for soybean maturity groups

Langewisch¹,

Lenis²,

Jiang³

et al. 2017

BMC Plant Biol

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BackgroundAchieving appropriate maturity in a target environment is essential to maximizing crop yield potential. In soybean [Glycine max (L.) Merr.], the time to maturity is largely dependent on developmental response to dark periods. Once the critical photoperiod is reached, flowering is initiated and reproductive development proceeds. Therefore, soybean adaptation has been attributed to genetic changes and natural or artificial selection to optimize plant development in specific, narrow latitudinal ranges. In North America, these regions have been classified into twelve maturity groups (MG), with lower MG being shorter season than higher MG. Growing soybean lines not adapted to a particular environment typically results in poor growth and significant yield reductions. The objective of this study was to develop a molecular model for soybean maturity based on the alleles underlying the major maturity loci: E1, E2, and E3.ResultsWe determined the allelic variation and diversity of the E maturity genes in a large collection of soybean landraces, North American ancestors, Chinese cultivars, North American cultivars or expired Plant Variety Protection lines, and private-company lines. The E gene status of accessions in the USDA Soybean Germplasm Collection with SoySNP50K Beadchip data was also predicted. We determined the E allelic combinations needed to adapt soybean to different MGs in the United States (US) and discovered a strong signal of selection for E genotypes released in North America, particularly the US and Canada.ConclusionsThe E gene maturity model proposed will enable plant breeders to more effectively transfer traits into different MGs and increase the overall efficiency of soybean breeding in the US and Canada. The powerful yet simple selection strategy for increasing soybean breeding efficiency can be used alone or to directly enhance genomic prediction/selection schemes. The results also revealed previously unrecognized aspects of artificial selection in soybean imposed by soybean breeders based on geography that highlights the need for plant breeding that is optimized for specific environments.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-017-1040-4) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

The development and use of a molecular model for soybean maturity groups

Langewisch¹,

Lenis²,

Jiang³

et al. 2017

BMC Plant Biol

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“…In this study, we used 300 rapeseed accessions collected from different regions of China with outgroups from other countries, to sequence genome-wide distributed specific locus amplified fragments (SLAF) for polymorphism detection and genotyping (Sun et al, 2013), with an average sequencing depth of 6.27-fold per accession (>5.0-fold), in order to assure the veracity of the population genetic analyses (He et al, 2011; Han et al, 2016). The mean physical distance between SNP markers was 0.22 Kb, which was dramatically shorter than the mean LD decay distance (298.95 Kb), so the density of SNP markers was sufficient for genetic diversity and association mapping purposes (Morris et al, 2013).…”

Section: Discussionmentioning

confidence: 99%

“…SNP markers have been used for a wide range of purposes in Brassica , including rapid identification of cultivars, QTL analysis, and construction of ultra-high-density genetic maps (Delourme et al, 2013). Moreover, SNPs provide valuable markers for the study of agronomic traits in crops via strategies such as genetic linkage mapping or association genetics (Han et al, 2016). …”

Section: Introductionmentioning

confidence: 99%

Genome-Wide SNP Markers Based on SLAF-Seq Uncover Breeding Traces in Rapeseed (Brassica napus L.)

Zhou

Zheng

et al. 2017

Front. Plant Sci.

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Single Nucleotide Polymorphisms (SNPs) are the most abundant and richest form of genomic polymorphism, and hence make highly favorable markers for genetic map construction and genome-wide association studies. In this study, a total of 300 rapeseed accessions (278 representative of Chinese germplasm, plus 22 outgroup accessions of different origins and ecotypes) were collected and sequenced using Specific-Locus Amplified Fragment Sequencing (SLAF-seq) technology, obtaining 660.25M reads with an average sequencing depth of 6.27 × and a mean Q30 of 85.96%. Based on the 238,711 polymorphic SLAF tags a total of 1,197,282 SNPs were discovered, and a subset of 201,817 SNPs with minor allele frequency >0.05 and integrity >0.8 were selected. Of these, 30,877 were designated SNP “hotspots,” and 41 SNP-rich genomic regions could be delineated, with 100 genes associated with plant resistance, vernalization response, and signal transduction detected in these regions. Subsequent analysis of genetic diversity, linkage disequilibrium (LD), and population structure in the 300 accessions was carried out based on the 201,817 SNPs. Nine subpopulations were observed based on the population structure analysis. Hierarchical clustering and principal component analysis divided the 300 varieties roughly in accordance with their ecotype origins. However, spring-type varieties were intermingled with semi-winter type varieties, indicating frequent hybridization between spring and semi-winter ecotypes in China. In addition, LD decay across the whole genome averaged 299 kb when r2 = 0.1, but the LD decay in the A genome (43 kb) was much shorter than in the C genome (1,455 kb), supporting the targeted introgression of the A genome from progenitor species B. rapa into Chinese rapeseed. This study also lays the foundation for genetic analysis of important agronomic traits using this rapeseed population.

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“…The π values of this tree species ranged from 0.0010 to 0.0016 among different populations[51], which is very similar to the estimated Sanqi range. The genomic nucleotide diversity of cultivated soybean ( Glycine max ) was 0.0005 ~ 0.0010[52], as estimated by SLAF-seq, which is another reduced-representation sequencing technology similar to RAD sequencing [53]; the estimated values were even lower than those of P . notoginseng and P .…”

Section: Discussionmentioning

confidence: 99%

Application of RAD Sequencing for Evaluating the Genetic Diversity of Domesticated Panax notoginseng (Araliaceae)

Pan

Wang

Sun³

et al. 2016

PLoS ONE

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Panax notoginseng, a traditional Chinese medicinal plant, has been cultivated and domesticated for approximately 400 years, mainly in Yunnan and Guangxi, two provinces in southwest China. This species was named according to cultivated rather than wild individuals, and no wild populations had been found until now. The genetic resources available on farms are important for both breeding practices and resource conservation. In the present study, the recently developed technology RADseq, which is based on next-generation sequencing, was used to analyze the genetic variation and differentiation of P. notoginseng. The nucleotide diversity and heterozygosity results indicated that P. notoginseng had low genetic diversity at both the species and population levels. Almost no genetic differentiation has been detected, and all populations were genetically similar due to strong gene flow and insufficient splitting time. Although the genetic diversity of P. notoginseng was low at both species and population levels, several traditional plantations had relatively high genetic diversity, as revealed by the He and π values and by the private allele numbers. These valuable genetic resources should be protected as soon as possible to facilitate future breeding projects. The possible geographical origin of Sanqi domestication was discussed based on the results of the genetic diversity analysis.

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Domestication footprints anchor genomic regions of agronomic importance in soybeans

Cited by 132 publications

References 46 publications

The development and use of a molecular model for soybean maturity groups

The development and use of a molecular model for soybean maturity groups

Genome-Wide SNP Markers Based on SLAF-Seq Uncover Breeding Traces in Rapeseed (Brassica napus L.)

Application of RAD Sequencing for Evaluating the Genetic Diversity of Domesticated Panax notoginseng (Araliaceae)

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