A near‐complete genome sequence of mungbean (<i>Vigna radiata</i> L.) provides key insights into the modern breeding program

Ha, Jung Min; Satyawan, Dani; Jeong, Haneul; Lee, Eunsoo; Cho, Kang-Heum; Kim, Moon Young; Lee, Suk-Ha

doi:10.1002/tpg2.20121

Cited by 38 publications

(57 citation statements)

References 70 publications

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“…Our results showed that another feature of Baekdadagi-specific genetically diverse genomic regions is maintenance of genetic diversity; however, this diversity was not distributed evenly across the cucumber genomes. These results are consistent with selective sweep events which happened during domestication and modern breeding in mung bean and lettuce [38,39]. Putative selective sweep regions of both crops were also not distributed evenly.…”

Section: Discussionsupporting

confidence: 80%

Development of SNP Marker Sets for Marker-Assisted Background Selection in Cultivated Cucumber Varieties

et al. 2022

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Marker-assisted background selection is a powerful molecular tool that can enhance breeding efficiency through the analysis of a large number of markers representing the entire genomic background for precise selection. In the present study, the transcriptomes of 38 cucumber inbred lines with diverse traits were sequenced for single nucleotide polymorphism (SNP) mining for practical application to commercial cucumber breeding. A total of 62,378 high-quality SNPs were identified, of which 2462 SNPs were chosen based on the stringent filtering parameters. Finally, 363 evenly distributed common background selection markers (BMs) were developed and validated through polymorphism analysis and phylogenetic analysis using breeding materials with different genetic backgrounds; 327 out of 363 common BMs were useful for background selection. Moreover, the results of the phylogenetic analysis carried out using 50 selected core BMs were consistent with those for 327 common BMs. However, when the genotypes of breeding materials belonging to only the Baekdadagi-type were analyzed, the 327 common BMs showed a significant reduction in polymorphisms within the biased genomic locations. To address this issue, 59 highly polymorphic markers were selected as Baekdadagi BMs, as they showed better selection ability for the Baekdadagi-type. The 327 common BMs developed in the present study will enable efficient marker-assisted background selection in cucumber. Additionally, to reduce the genotyping cost, we suggested an alternative background selection strategy using both evenly distributed core BMs and biased Baekdadagi BMs for the improvement of commercial cucumber breeding programs.

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Section: Discussionsupporting

confidence: 80%

Development of SNP Marker Sets for Marker-Assisted Background Selection in Cultivated Cucumber Varieties

et al. 2022

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“…The appreciable difference in FreeBayes QV between the two assemblies still points towards a higher error rate in the TGACv2 reference, and suggests that the ARS_RCv1.1 assembly is more suitable as a reference for short-read WGS alignment in the red clover species. The MedTr4 assembly represents a high-quality reference for most legume species, and has been used in several whole genome comparisons to indicate assembly quality [39,40]. This includes the original release of the TGACv2 reference, where synteny was identified between MedTr4 and the TGACv2 assembly [14].…”

Section: Data Validation and Quality Control Assembly Error-rate Asse...mentioning

confidence: 99%

Chromosome-scale assembly of the highly heterozygous genome of red clover (Trifolium pratense L.), an allogamous forage crop species

et al. 2022

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Relative to other crops, red clover (Trifolium pratense L.) has various favorable traits making it an ideal forage crop. Conventional breeding has improved varieties, but modern genomic methods could accelerate progress and facilitate gene discovery. Existing short-read-based genome assemblies of the ∼420 megabase pair (Mbp) genome are fragmented into >135,000 contigs, with numerous order and orientation errors within scaffolds, probably associated with the plant's biology, which displays gametophytic self-incompatibility resulting in inherent high heterozygosity. Here, we present a high-quality long-read-based assembly of red clover with a more than 500-fold reduction in contigs, improved per-base quality, and increased contig N50 by three orders of magnitude. The 413.5 Mbp assembly is nearly 20% longer than the 350 Mbp short-read assembly, closer to the predicted genome size. We also present quality measures and full-length isoform RNA transcript sequences for assessing accuracy and future genome annotation. The assembly accurately represents the seven main linkage groups in an allogamous (outcrossing), highly heterozygous plant genome. Subjects Genetics and Genomics, Bioinformatics, Plant Genetics DATA DESCRIPTION BackgroundThe species Trifolium pratense L. (red clover, NCBI:txid57577) is an important legume forage crop grown on approximately 4 million hectares worldwide [1]. Red clover is a versatile crop grown as animal feed and/or as a green manure in pure and mixed stands for hay, haylage, silage, and grazing. Red clover is known for its ease of establishment and shade tolerance, and its ability to grow in poorly drained and low pH soils. The reduced need for exogenous nitrogen application owing to its nitrogen-fixing ability and the relatively high protein content of this plant compared with other forage crops provide potential for reducing the environmental footprint of livestock production. Compared to alfalfa, another common legume forage crop, red clover varieties have higher forage yields, are a better source of magnesium to avoid grass tetany in grazing cattle, and may have improved post-harvest protein preservation [2] and bypass protein content in ruminant production

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“…The MedTr4 assembly represents a high quality reference for most legume species, and has been used in several whole genome comparisons to indicate assembly quality [31,32]. This includes the original release of the TGACv2 reference, where synteny was identified between MedTr4 and the TGACv2 assembly [14].…”

Section: Data Validation and Quality Controlmentioning

confidence: 99%

Chromosome-scale assembly of the highly heterozygous genome of red clover (Trifolium pratense L.), an allogamous forage crop species

Bickhart

Koch

Smith

et al. 2022

Preprint

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Red clover (Trifolium pratense L.) is used as a forage crop due to a variety of favorable traits relative to other crops. Improved varieties have been developed through conventional breeding approaches, but progress could be accelerated and gene discovery facilitated using modern genomic methods. Existing short-read based genome assemblies of the ~420 Megabase (Mb) genome are fragmented into >135,000 contigs with numerous errors in order and orientation within scaffolds, likely due to the biology of the plant which displays gametophytic self-incompatibility resulting in inherent high heterozygosity. A high-quality long-read based assembly of red clover is presented that reduces the number of contigs by more than 500-fold, improves the per-base quality, and increases the contig N50 statistic by three orders of magnitude. The 413.5 Mb assembly is nearly 20% longer than the 350 Mb short read assembly, closer to the predicted genome size. Quality measures are presented and full-length isoform sequence of RNA transcripts reported for use in assessing accuracy and for future annotation of the genome. The assembly accurately represents the seven main linkage groups present in the genome of an allogamous (outcrossing), highly heterozygous plant species.

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A near‐complete genome sequence of mungbean (Vigna radiata L.) provides key insights into the modern breeding program

Cited by 38 publications

References 70 publications

Development of SNP Marker Sets for Marker-Assisted Background Selection in Cultivated Cucumber Varieties

Development of SNP Marker Sets for Marker-Assisted Background Selection in Cultivated Cucumber Varieties

Chromosome-scale assembly of the highly heterozygous genome of red clover (Trifolium pratense L.), an allogamous forage crop species

Chromosome-scale assembly of the highly heterozygous genome of red clover (Trifolium pratense L.), an allogamous forage crop species

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