Identification of genomic regions conferring rust resistance and enhanced mineral accumulation in a HarvestPlus Association Mapping Panel of wheat

AbstractWe used three approaches to map the yellow rust resistance gene Yr7 and identify associated SNPs in wheat. First, we used a traditional QTL mapping approach using a double haploid (DH) population and mapped Yr7 to a low-recombination region of chromosome 2B. To fine map the QTL, we then used an association mapping panel. Both populations were SNP array genotyped allowing alignment of QTL and genome-wide association scans based on common segregating SNPs. Analysis of the association panel spanning the QTL interval, narrowed the interval down to a single haplotype block. Finally, we used mapping-by-sequencing of resistant and susceptible DH bulks to identify a candidate gene in the interval showing high homology to a previously suggested Yr7 candidate and to populate the Yr7 interval with a higher density of polymorphisms. We highlight the power of combining mapping-by-sequencing, delivering a complete list of gene-based segregating polymorphisms in the interval with the high recombination, low LD precision of the association mapping panel. Our mapping-by-sequencing methodology is applicable to any trait and our results validate the approach in wheat, where with a near complete reference genome sequence, we are able to define a small interval containing the causative gene.HighlightWe show progression from genetic mapping to mapping-by-sequencing and the overlap of defined intervals by each approach culminating with interval refinement and identification of a candidate gene for disease resistance.

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A genomewide association mapping study using ultrasound-scanned information identifies potential genomic regions and candidate genes affecting carcass traits in Nellore cattle

Journal of Animal Breeding and Genetics ◽

10.1111/jbg.12167 ◽

2015 ◽

Vol 132 (6) ◽

pp. 420-427 ◽

Cited By ~ 16

Author(s):

M.H.A. Santana ◽

R.V. Ventura ◽

Y.T. Utsunomiya ◽

H.H.R. Neves ◽

P.A. Alexandre ◽

...

Keyword(s):

Association Mapping ◽

Candidate Genes ◽

Carcass Traits ◽

Mapping Study ◽

Nellore Cattle ◽

Genomewide Association ◽

Association Mapping Study ◽

Genomic Regions

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Association Mapping of Seedling and Adult Plant Resistance for Stripe Rust Resistance in Spring Bread Wheat (Triticum aestivum L.)

Advances in Crop Science and Technology ◽

10.4172/2329-8863.1000383 ◽

2018 ◽

Vol 06 (04) ◽

Cited By ~ 1

Author(s):

Yewubdar Shewaye ◽

Wuletaw Taddesse

Keyword(s):

Triticum Aestivum ◽

Association Mapping ◽

Bread Wheat ◽

Plant Resistance ◽

Rust Resistance ◽

Adult Plant Resistance ◽

Triticum Aestivum L ◽

Stripe Rust Resistance ◽

Adult Plant ◽

Spring Bread Wheat

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Dissection of the genetic basis of oil content in Chinese peanut cultivars through association mapping

10.21203/rs.3.rs-17113/v2 ◽

2020 ◽

Author(s):

Nian Liu ◽

Li Huang ◽

Weigang Chen ◽

Bei Wu ◽

Manish K. Pandey ◽

...

Keyword(s):

Association Mapping ◽

Ssr Markers ◽

Oil Content ◽

Genetic Basis ◽

Principal Component ◽

Primary Sources ◽

Phenotypic Variance ◽

Mapping Panel ◽

Stable Association ◽

Faster Development

Abstract Background: Peanut is one of the primary sources for vegetable oil worldwide, and enhancing oil content is the main objective in several peanut breeding programs of the world. Tightly linked markers are required for faster development of high oil content peanut varieties through genomics-assisted breeding (GAB), and association mapping is one of the promising approaches for discovery of such associated markers. Results: An association mapping panel consisting of 292 peanut varieties extensively distributed in China was phenotyped for oil content and genotyped with 583 polymorphic SSR markers. These markers amplified 3663 alleles with an average of 6.28 alleles per locus. The structure, phylogenetic relationship, and principal component analysis (PCA) indicated two subgroups majorly differentiating based on geographic regions. Genome-wide association analysis identified 12 associated markers including one (AGGS1014_2) highly stable association controlling up to 9.94% phenotypic variance explained (PVE) across multiple environments. Interestingly, the frequency of the favorable alleles for 12 associated markers showed a geographic difference. Two associated markers (AGGS1014_2 and AHGS0798) with 6.90-9.94% PVE were verified to enhance oil content in an independent RIL population and also indicated selection during the breeding program. Conclusion: This study provided insights into the genetic basis of oil content in peanut and verified highly associated two SSR markers to facilitate marker-assisted selection for developing high-oil content breeding peanut varieties.

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Comparative mapping of the two wheat leaf rust resistance loci Lr1 and Lr10 in rice and barley

Genome ◽

10.1139/g98-024 ◽

1998 ◽

Vol 41 (3) ◽

pp. 328-336 ◽

Cited By ~ 29

Author(s):

Francesca Gallego ◽

Catherine Feuillet ◽

Monika Messmer ◽

Anja Penger ◽

Andreas Graner ◽

...

Keyword(s):

Leaf Rust ◽

Comparative Mapping ◽

Rust Resistance ◽

Repetitive Sequences ◽

Rice Chromosome ◽

Leaf Rust Resistance ◽

Chromosome 1 ◽

Wheat Leaf Rust ◽

Wheat Leaf ◽

Genomic Regions

The wheat genome is large, hexaploid, and contains a high amount of repetitive sequences. In order to isolate agronomically important genes from wheat by map-based cloning, a simpler model of the genome must be used for identifying candidate genes. The objective of this study was to comparatively map the genomic regions of two wheat leaf rust disease resistance loci, Lr1 and Lr10, in the putative model genomes of rice and barley. Two probes cosegregating with the Lr1 gene on chromosome 5DL of wheat were studied. The rice sequences corresponding to the two probes were isolated and mapped. The two probes mapped to two different rice chromosomes, indicating that the organization of the region orthologous to Lr1 is different in rice and wheat. In contrast, synteny was conserved between wheat and barley in this chromosomal region. The Lrk10 gene cosegregated with Lr10 on chromosome 1AS in wheat. The rice gene corresponding to Lrk10 was mapped on rice chromosome 1, where it occurred in many copies. This region on rice chromosome 1 corresponds to the distal part of the group 3S chromosomes in Triticeae. The synteny is conserved between rice chromosome 1 and the Triticeae group 3S chromosomes up to the telomere of the chromosomes. On group 3S chromosomes, we found a gene that is partially homologous to Lrk10. We conclude that in the genomic regions studied, there is limited and only partially useful synteny between wheat and rice. Therefore, barley should also be considered as a model genome for isolating the Lr1 and Lr10 genes from wheat.Key words: barley, comparative mapping, leaf rust, resistance genes, rice, synteny, wheat.

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