association mapping

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ZAIM
University of Mohammed V/ICARDA
Co-authors: 
HAFSSA,KABBAJ, AYED, AL ABDALLAT, GREGOR, GORJANC, JESSE, POLAND, MIKAEL, MILOUDI NACHIT, AHMED, AMRI, BOUCHRA, BELKADI, KARIM, FILALI MALTOUF, FILIPPO, BASSI MARIA, , , , , , , , , , , ,
Poster or Plenary?: 
Poster
BGRI Year: 
2018
Primary Author First Name: 
MERYEM

Durum wheat (Triticum durum Desf.) is a major stable crop and it represents a base of the Mediterranean diet. This region is subject to a Mediterranean climate, which is extremely unpredictable with severe changes in moisture and temperature occurring each crop season. This unpredictability is summarized by breeders as GxE and the identification of traits controlling this interaction is quintessential to ensure stability in production season after season. To study the genetics of yield stability, four RILs populations derived from elite x elite crosses were assessed for yield and 1,000-kernel weights across five diverging environments in Morocco and Lebanon. These 550 RILs were characterized with 4,909 polymorphic SNPs via genotyping by sequencing. A consensus map was derived by merging the individual genetic maps of each population. Finally, imputation was used to fill all the missing haplotypes and reach a reduction of missing data to below 8%. Several significant QTLs were identified to be linked to TKW, grain yield and a stability index, namely AMMI wide adaptation index (AWAI). A second approach to identify loci controlling stability was the use of a global panel of 288 elites, accessions and landraces tested in 15 diverging environment. Multi-locations data were compiled via GxE models to derive the AWAI stability index. In addition, this panel was characterized with 8,173 polymorphic SNPs via Axiom 35K array. Significant associations were identified for all traits, including QTLs unique to AWAI. The sum of the identified QTLs can now be pyramid via marker assisted selection and molecular designed crosses in order to obtain very stable cultivars.

Silva
INIA Uruguay and Dep. Plant Pathology, Kansas State University, US
Co-authors: 
Pierina Clerici, Richard Garcia, Fernando Pereira, Noelia Perez, Martin Quincke, Silvia German
Poster or Plenary?: 
Poster
BGRI Year: 
2018
Abstract Tags: 
Primary Author First Name: 
Paula

Leaf rust (LR) and stem rust (SR) are threats to global wheat production and new races frequently overcome resistance genes deployed in wheat cultivars. Identification of new sources of resistance is a major goal for many pre-breeding programs. The objective of this study was to investigate the genetic basis of resistance to LR and SR in a diverse South American wheat panel. Molecular markers for known resistance genes and GBS were used to dissect genetic components. The wheat panel of 122 lines was characterized under field conditions at La Estanzuela Research Station, Uruguay, for disease severity (DS) to LR (2014 and 2015) and SR (2015), and LTN (leaf tip necrosis). Final DS for LR ranged between 0 and 95%, with mean values of 40% (2014) and 46% (2015). For SR, final DS ranged between 0 and 50%, with a mean value of 5%. The frequencies of positive diagnostic resistance markers among accessions were 20.5% for Lr34/Sr57, 6.6% for Lr68, 3.3% for Sr2/Lr27, 23% for Sr31/Lr26, 20.5% for Sr24/Lr24, 9.4% for Sr25/Lr19, and 0% for Sr39/Lr35. Of all the LR/SR resistance genes, only the effect of Lr68 was significant when predicting LR DS. Seventeen lines were identified with combinations of two genes, but no combination conferred a significantly improved level of resistance. Preliminary GWAS analysis for LR response on a subset of 86 lines revealed several QTLs, with a major QTL explained by Lr68. Lines with good levels of resistance to LR and SR, high expression of LTN, and absence of markers for the studied resistance genes were identified, indicating that there are other genes involved in resistance. Future research involving the testing of additional molecular markers for other known resistance genes, and a deeper GWAS analysis, will provide further information about the resistance genes present in this wheat panel.

Ziems
The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, Australia
Primary Author Email: 
ziems@uq.edu.au

Elite barley breeding lines from the Australian Northern Region Barley Breeding Program were evaluated at the seedling and adult growth stages for resistance to leaf rust (LR) caused by Puccinia hordei. F3:5 lines derived from parental germplasm of different geographic origins were screened in the glasshouse and field spanning four years of trials. The 2009 and 2011 breeding populations (BP1 and BP2) comprised 360 lines and were genotyped with 3,244 polymorphic diversity arrays technology (DArT) markers. The 2012 and 2013 breeding populations (BP3 and BP4) comprised 320 lines genotyped with the DArT GBS array (DArTseq), providing 15,400 high quality polymorphic markers. Association mapping (AM) using the DArT/DArT-seq datasets and phenotypic data from 15 independent LR response assays identified a number of genomic regions associated with resistance. The BP1 and BP2 study detected a total of 15 QTL; 5 QTL co-located with catalogued LR resistance genes (Rph1, Rph3/19, Rph8/14/15, Rph20, and Rph21), 6 QTL aligned with previously reported genomic regions and 4 QTL (3 on chromosome 1H and 1 on 7H) were novel. Markers in common between the DArT and DArTseq datasets enabled integration of mapping results for LR response across the four breeding populations and all QTL detected were visualised on a single map for validation. The adult plant resistance (APR) locus Rph20 was the only region detected in all field environments. Markers and their associated sequences identified in this study will be useful for building QTL combinations involving Rph20, thereby providing stable LR resistance in improved barley cultivars. We will also highlight the advantages of AM using breeding germplasm over traditional bi-parental mapping approaches that underutilise genetic diversity and divert valuable resources into populations of low breeding value.

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