Genomic-assisted haplotype analysis and the development of high-throughput SNP markers for salinity tolerance in soybean

Patil, Gunvant; Do, Tuyen; Vuong, Tri D.; Valliyodan, Babu; Lee, Jeong Dong; Chaudhary, Juhi; Shannon, J. Grover; Nguyen, Henry T.

doi:10.1038/srep19199

Cited by 166 publications

(182 citation statements)

References 83 publications

Supporting

Mentioning

173

Contrasting

Order By: Relevance

“…This approach is demonstrated by the identification of new loci that are associated with tolerance of salinity using lowcoverage sequencing of 106 diverse soya bean (Glycine max) lines 84 and by exome sequencing from several wheat lines 85 . Genetically structured populations, genetic-association analyses and targeted sequencing can be used to define new haplotypes with greater variation, fewer deleterious alleles and improved phenotypes for incorporation into breeding programmes 68 .…”

Section: Crop Breeding As a Dna-assembly Problemmentioning

confidence: 99%

Genomic innovation for crop improvement

Bevan

Uauy

Wulff

et al. 2017

Nature

341

240

View full text Add to dashboard Cite

Crop production needs to increase to secure future food supplies, while reducing its impact on ecosystems. Detailed characterization of plant genome structure and genetic diversity is crucial for meeting these challenges. Advances in genome sequencing and assembly are being used to access to the large and complex genomes of crops and their wild relatives. Sequencing of wild crop relatives is identifying a wide spectrum of genetic variation, permitting the association of genetic diversity with diverse agronomic phenotypes. In combination with improved and automated phenotyping assays and functional genomic studies, genomics is providing new foundations for crop-breeding systems. In the twentieth century, famines caused by political crises, mismanagement of food production or genocide killed an estimated 70 million people and were second only to war as the greatest manmade cause of death 1 . The father of the Green Revolution, Norman Borlaug, summarized the importance of crops: "Without food, people perish, social and political organizations disintegrate, and civilizations collapse. " For thousands of years, people have dedicated considerable resources to securing food supplies; for example, grain supplies to ancient Rome were secured through an extensive network of long-distance transport, and the distribution of grain was coordinated and subsidized by the cura annonae ('care for the grain supply'), an important figure who contributed to the maintenance of political unity and power.During the past 10,000 years, a period known as the Holocene, Earth's environment has been unusually stable. This probably facilitated the domestication of crops from wild species, resulting in steadily improved yields and adaptation to new agricultural areas. The production of food is now carried out on a vast scale, with 38% of Earth's surface dedicated to agriculture 2 . This increased production is having a pervasive influence on ecosystems worldwide: nitrogen production for agriculture accounts for 1.2% of global energy consumption 3 ; photosynthesis can no longer maintain stable levels of atmospheric carbon dioxide; and food production consumes around 70% of freshwater supplies. The modelling of crop responses to increases in temperature predicts that there will be a considerable reduction in the yield of rice, an important crop around the world 4 . Climate change could also alter the dynamics of crop pathogenic agents by altering the range of vectors and by compromising the immune response of crops 5 .Crop production must therefore adapt to more variable environments and the substantial impact it has on the environment needs to be reduced. Productivity must also increase at a much greater rate than in the past to meet the needs of Earth's growing population 6 . Genetic improvements in crop performance continue to be crucial for increasing crop productivity, but current rates of improvement are unable to meet the demands of sustainability and food security 7 . Plant genomics has a central role in the improvement of crops, includi...

show abstract

Section: Crop Breeding As a Dna-assembly Problemmentioning

confidence: 99%

Genomic innovation for crop improvement

Bevan

Uauy

Wulff

et al. 2017

Nature

341

240

View full text Add to dashboard Cite

show abstract

“…Diagnostic markers were confirmed to be workable on a broad range of commercial lupin cultivars (Yang et al 2015). Haplotype contigs (haplotigs) associated with soybean salinity were identified through whole-genome re-sequencing (Patil et al 2016), which was applicated to the prediction of salt-tolerant/ sensitive genotypes. Markers that define the haplotig could be assembled to form a genome-wide set of markers (Chin et al 2016).…”

Section: Genome Sequencing and Sequencebased Markersmentioning

confidence: 99%

Genomics-assisted breeding – A revolutionary strategy for crop improvement

Leng

Lübberstedt

2017

Journal of Integrative Agriculture

View full text Add to dashboard Cite

Food shortages arise more frequently owing to unpredictable crop yield losses caused by biotic and abiotic stresses. With advances in molecular biology and marker technology, a new era of molecular breeding has emerged that has greatly accelerated the pace of plant breeding. High-throughput genotyping technology and phenotyping platforms have enabled large-scale marker-trait association analysis, such as genome-wide association studies, to precisely dissect the genetic architecture of plant traits. Large-scale mapping of agronomically important quantitative trait loci, gene cloning and characterization, mining of elite alleles/ haplotypes, exploitation of natural variations, and genomic selection have paved the way towards genomicsassisted breeding (GAB). With the availability of more and more informative genomic datasets, GAB would become a promising technique to expedite the breeding cycle for crop improvement. AbstractFood shortages arise more frequently owing to unpredictable crop yield losses caused by biotic and abiotic stresses. With advances in molecular biology and marker technology, a new era of molecular breeding has emerged that has greatly accelerated the pace of plant breeding. High-throughput genotyping technology and phenotyping platforms have enabled large-scale marker-trait association analysis, such as genome-wide association studies, to precisely dissect the genetic architecture of plant traits. Large-scale mapping of agronomically important quantitative trait loci, gene cloning and characterization, mining of elite alleles/haplotypes, exploitation of natural variations, and genomic selection have paved the way towards genomics-assisted breeding (GAB). With the availability of more and more informative genomic datasets, GAB would become a promising technique to expedite the breeding cycle for crop improvement.

show abstract

“…All of the characterized genes underlying salt tolerant QTLs were pinpointed at single gene Glyma03g32900 , and the presence of Ty1/copia type retrotransposon in all salt tolerant genotypes indicate the single point of origin for salt sensitivity in soybean. Patil et al (2016) used whole genome re-sequencing data for haplotype analysis of the GmCHX1 gene ( Glyma03g32900 ) identifying three major structural variants and allelic variation in the promoter and genic regions. Based on SNPs specific to three structural variants, breeder friendly KASPar assays have been developed and validated which will be very useful for molecular breeding for salt tolerance in soybean (Patil et al, 2016).…”

Section: Qtlomics: Qtls To Genes In Soybeanmentioning

confidence: 99%

“…Patil et al (2016) used whole genome re-sequencing data for haplotype analysis of the GmCHX1 gene ( Glyma03g32900 ) identifying three major structural variants and allelic variation in the promoter and genic regions. Based on SNPs specific to three structural variants, breeder friendly KASPar assays have been developed and validated which will be very useful for molecular breeding for salt tolerance in soybean (Patil et al, 2016). …”

Section: Qtlomics: Qtls To Genes In Soybeanmentioning

confidence: 99%

“…These are some examples which demonstrate the utility of functional markers developed by characterization of underlying genes of specific traits, to harness the true benefits of translational genomics and breeding in soybean. Although, the functional markers used in the above cited examples were not developed by QTL mapping and characterization, however several functional markers have been recently developed based on characterization of genes underlying QTLs and currently has been utilized in ongoing soybean breeding programs (Tsubokura et al, 2013; Xu et al, 2013; Tardivel et al, 2014; Kadam et al, 2016; Patil et al, 2016). …”

Section: Prospectus Of Translational Genomics and Breeding In Soybeanmentioning

confidence: 99%

See 1 more Smart Citation

QTLomics in Soybean: A Way Forward for Translational Genomics and Breeding

et al. 2016

View full text Add to dashboard Cite

Food legumes play an important role in attaining both food and nutritional security along with sustainable agricultural production for the well-being of humans globally. The various traits of economic importance in legume crops are complex and quantitative in nature, which are governed by quantitative trait loci (QTLs). Mapping of quantitative traits is a tedious and costly process, however, a large number of QTLs has been mapped in soybean for various traits albeit their utilization in breeding programmes is poorly reported. For their effective use in breeding programme it is imperative to narrow down the confidence interval of QTLs, to identify the underlying genes, and most importantly allelic characterization of these genes for identifying superior variants. In the field of functional genomics, especially in the identification and characterization of gene responsible for quantitative traits, soybean is far ahead from other legume crops. The availability of genic information about quantitative traits is more significant because it is easy and effective to identify homologs than identifying shared syntenic regions in other crop species. In soybean, genes underlying QTLs have been identified and functionally characterized for phosphorous efficiency, flowering and maturity, pod dehiscence, hard-seededness, α-Tocopherol content, soybean cyst nematode, sudden death syndrome, and salt tolerance. Candidate genes have also been identified for many other quantitative traits for which functional validation is required. Using the sequence information of identified genes from soybean, comparative genomic analysis of homologs in other legume crops could discover novel structural variants and useful alleles for functional marker development. The functional markers may be very useful for molecular breeding in soybean and harnessing benefit of translational research from soybean to other leguminous crops. Thus, soybean crop can act as a model crop for translational genomics and breeding of quantitative traits in legume crops. In this review, we summarize current status of identification and characterization of genes underlying QTLs for various quantitative traits in soybean and their significance in translational genomics and breeding of other legume crops.

show abstract

Genomic-assisted haplotype analysis and the development of high-throughput SNP markers for salinity tolerance in soybean

Cited by 166 publications

References 83 publications

Genomic innovation for crop improvement

Genomic innovation for crop improvement

Genomics-assisted breeding – A revolutionary strategy for crop improvement

QTLomics in Soybean: A Way Forward for Translational Genomics and Breeding

Contact Info

Product

Resources

About