Posts Tagged ‘Quantitative trait loci’

Identification of Genomic Associations for Adult Plant Resistance in the Background of Popular South Asian Wheat Cultivar, PBW343

Posted by gabrielamartinez on , in Journal Articles

Rusts, a fungal disease as old as its host plant wheat, an enemy as old as wheat, has caused havoc for over 8,000 years. As the rust pathogens can evolve into new virulent races which quickly defeat to qualitative or vertical the resistance that primarily rely on race specificity over time, adult plant resistance (APR) has often been found to be race non-specific and hence is considered have been proven to be a more to be a more reliable and durable strategy to combat this malady. Over decades sets of donor lines have been identified at International Maize and Wheat Improvement Center (CIMMYT) representing a wide range of APR sources in wheat. In this study, using nine donors and a common parent ‘PBW343’, a popular Green Revolution variety at CIMMYT, the nested association mapping (NAM) population of 1122 lines was constructed to understand the APR genetics underlying these founder lines. Thirty-four QTL were associated with APR to rusts, and 20 of 34 QTL had pleiotropic effects on SR, YR and LR resistance. Three chromosomal regions, associated with known APR genes (Sr58/Yr29/Lr46, Sr2/Yr30/Lr27, and Sr57/Yr18/Lr34), were also identified, 13 previously reported QTL regions were validated. Of the 18 QTL first detected in this study, 7 were pleiotropic QTL, distributing on chromosomes 3A, 3B, 6B, 3D, and 6D. The present investigation revealed the genetic relationship of historical APR donor lines, the novel knowledge on APR, as well as the new analytical methodologies to facilitate the applications of NAM design in crop genetics. Results shown in this study will aid the parental selection for hybridization in wheat breeding, and envision the future rust management breeding for addressing potential threat to wheat production and food security.

Source: Frontiers | Identification of Genomic Associations for Adult Plant Resistance in the Background of Popular South Asian Wheat Cultivar, PBW343 | Plant Science

Identification of Genomic Associations for Adult Plant Resistance in the Background of Popular South Asian Wheat Cultivar, PBW343

Posted by gabrielamartinez on , in Journal Articles

Rusts, a fungal disease as old as its host plant wheat, an enemy as old as wheat, has caused havoc for over 8,000 years. As the rust pathogens can evolve into new virulent races which quickly defeat to qualitative or vertical the resistance that primarily rely on race specificity over time, adult plant resistance (APR) has often been found to be race non-specific and hence is considered have been proven to be a more to be a more reliable and durable strategy to combat this malady. Over decades sets of donor lines have been identified at International Maize and Wheat Improvement Center (CIMMYT) representing a wide range of APR sources in wheat. In this study, using nine donors and a common parent ‘PBW343’, a popular Green Revolution variety at CIMMYT, the nested association mapping (NAM) population of 1122 lines was constructed to understand the APR genetics underlying these founder lines. Thirty-four QTL were associated with APR to rusts, and 20 of 34 QTL had pleiotropic effects on SR, YR and LR resistance. Three chromosomal regions, associated with known APR genes (Sr58/Yr29/Lr46, Sr2/Yr30/Lr27, and Sr57/Yr18/Lr34), were also identified, 13 previously reported QTL regions were validated. Of the 18 QTL first detected in this study, 7 were pleiotropic QTL, distributing on chromosomes 3A, 3B, 6B, 3D, and 6D. The present investigation revealed the genetic relationship of historical APR donor lines, the novel knowledge on APR, as well as the new analytical methodologies to facilitate the applications of NAM design in crop genetics. Results shown in this study will aid the parental selection for hybridization in wheat breeding, and envision the future rust management breeding for addressing potential threat to wheat production and food security.

Source: Frontiers | Identification of Genomic Associations for Adult Plant Resistance in the Background of Popular South Asian Wheat Cultivar, PBW343 | Plant Genetics and Genomics

Molecular mapping of high temperature tolerance in bread wheat adapted to the Eastern Gangetic Plain region of India

Posted by Carelia Juarez on , in Journal Articles

Published in Field Crops Research, 2013

Tiwari, C.; Wallwork, H.; Kumar, U.; Dhari, R.; Arun, B.; Mishra, V.K.; Reynolds, M.P.; Joshi, A.K.

The inheritance of tolerance to high temperature stress during the grain filling period was investigated via a QTL analysis based on 138 doubled haploid progeny of a cross between the wheat cultivars Berkut and Krichauff. Performance data were collected from three seasons, in each of which the material was planted both at the conventional time and a month later. A heat sensitivity index (HSI) was also used to monitor the effect of high temperature on grain yield, thousand grain weight, grain filling duration and canopy temperature. Using composite interval mapping, seven stable QTL were identified for HSI of traits, mapping to chromosomes 1D, 6B, 2D and 7A. Three of the QTL related to HSI of grain filling duration, two to thousand grain weight and one each to grain yield and canopy temperature. A region of chromosome 1D harbored a QTL determining HSI of both thousand grain weight and canopy temperature. The QTL analysis for the direct traits GY, TGW, GFD and CT led to detection of 22 QTLs spread over to 17 chromosomal regions. Of these 13 QTLs were shown under normal sown, while 9 under the heat stress. A QTL for TGW on chromosome 6B under normal sown co-located with HSI(TGW) QTL QHTgw.bhu-6BL. QTL × environment interactions were not observed for any of the grain filling duration associated loci.

Root-lodging resistance in maize as an example for high-throughput genetic mapping via single nucleotide polymorphism-based selective genotyping

Posted by Carelia Juarez on , in Journal Articles

Published in Plant Breeding 132 (1) : 90-98, 2013

Mohammad Farkhari, Alan Krivanek, Yunbi Xu, Tingzhao Rong, Mohammad R. Naghavi, Bahman Y. Samadi and Yanli Lu

Large-scale selective genotyping and high-throughput analysis are two important strategies for low-cost and high-effective genetic mapping. In this study, selective genotyping was applied to four maize F2 populations. Thirty plants were selected from each of the two tails of the original F2 populations to represent extreme resistant and susceptible plants to root lodging, and genotyped individually with 1536 single nucleotide polymorphisms (SNPs). A quantitative trait locus (QTL) was declared when at least three closely linked SNPs showed significant allele frequency difference between the two tails. Nine QTL were identified for root lodging across the four populations, which were located on chromosomes 2, 4, 5, 7, 8 and 10 and one of them was shared between two populations. A total of 20 segregation distortion regions (SDRs) were identified across the four populations, one of which was co-localized with a QTL on chromosome 4. The tightly linked SNPs identified in this study can be used for marker-assisted selection for root lodging. Selective genotyping, when combined with pooled DNA analysis, can be used to develop strategies for high-throughput genetic mapping for all crops.

 

Confirming quantitative trait loci for aflatoxin resistance from Mp313E in different genetic backgrounds

Posted by Carelia Juarez on , in Journal Articles

Published in Molecular Breeding, 2013

Martha C. Willcox, Georgia L. Davis,  Marilyn L. Warburton,  Gary L. Windham, Hamed K. Abbas,  Javier Betrán, James B. Holland and W. Paul Williams

The fungus Aspergillus flavus (Link:Fr) causes ear rot of maize (Zea mays L.) and produces the toxic metabolic product aflatoxin. One particularly effective method of controlling the fungus is via host plant resistance, but while several resistant breeding lines have been identified, transferring the resistance genes from these lines into elite cultivars has been less effective than needed. A high number of genes involved with resistance, each with a small effect, and some only found under certain environmental conditions, has hampered resistance breeding. The identification of markers linked to genomic regions associated with resistance would aid in this effort. The goals of this study were to identify and characterize quantitative trait loci (QTL) conferring resistance to aflatoxin accumulation from resistant maize donor Mp313E in a background of the susceptible inbred line Va35; to compare them to the QTL identified from Mp313E in a background of B73; and to test the stability of the QTL identified in Mp313E × Va35 in multiple environments by remapping the phenotypic tails of the Mp313E × Va35 mapping population in new locations. Twenty different QTL were found in this study, 11 of which were also found in different environments using the phenotypic tail subset mapping population, and five of which were likely the same as those reported in the Mp313E × B73 mapping population. This indicates that many of the QTL are stable over the environments and genetic backgrounds tested, which will make them more valuable in breeding efforts.

Molecular mapping of quantitative trait loci for adult-plant resistance to powdery mildew in Italian wheat cultivar Libellula

Posted by Carelia Juarez on , in Journal Articles

Published in Crop and Pasture Science 63 (6) : 539-546, 2012

M. A. Asad , B. Bai , C. X. Lan , J. Yan , X. C. Xia , Y. Zhang  and Z. H. He

Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is a fungal disease that causes significant yield losses in many wheat-growing regions of the world. Previously, five quantitative trait loci (QTLs) for adult-plant resistance (APR) to stripe rust resistance were identified in Italian wheat cultivar Libellula. The objectives of this study were to map QTLs for APR to powdery mildew in 244 F2 : 3 lines of Libellula/Huixianhong, to analyse the stability of detected QTLs across environments, and to assess the association of these QTLs with stripe rust resistance. Powdery mildew response was evaluated for 2 years in Beijing and for 1 year in Anyang. The correlation between averaged maximum disease severity (MDS) and averaged area under disease progress curve (AUDPC) over 2 years in Beijing was 0.98, and heritabilities of MDS and AUDPC were 0.65 and 0.81, respectively, based on the mean values averaged across environments. SSR markers were used to screen the parents and mapping population. Five QTLs were identified by inclusive composite interval mapping, designated as QPm.caas2DS, QPm.caas4BL.1, QPm.caas6BL.1, QPm.caas6BL.2, and QPm.caas7DS. Three QTLs (QPm.caas2DS and QPm.caas6BL.1, and QPm.caas6BL.2) seem to be new resistance loci for powdery mildew. QTLs QPm.caas2DS and QPm.caas4BL.1 were identified at the same position as previously mapped QTLs for stripe rust resistance in Libellula. The QTL QPm.caas7DS, derived from Libellula, coincided with the slow rusting and slow mildewing locus Lr34/Yr18/Pm38. These results and the identified markers could be useful for wheat breeders aiming for durable resistance to both powdery mildew and stripe rust.