Posts Tagged ‘QTL mapping’

A high density GBS map of bread wheat and its application for dissecting complex disease resistance traits

Posted by gabrielamartinez on , in Journal Articles

56897Authors: Huihui Li, Vikram, P., Singh, R.P., Carling, J., Song, J., Burgueño, J., Bhavani, S., Huerta Espino, J., Payne, T.S., Sehgal, D., Wenzl, P., Sukhwinder-Singh.

Published in: BMC Genomics, 16: 216, 2015.


Background: Genotyping-by-sequencing (GBS) is a high-throughput genotyping approach that is starting to be used in several crop species, including bread wheat. Anchoring GBS tags on chromosomes is an important step towards utilizing them for wheat genetic improvement. Here we use genetic linkage mapping to construct a consensus map containing 28644 GBS markers.

Results: Three RIL populations, PBW343 × Kingbird, PBW343 × Kenya Swara and PBW343 × Muu, which share a common parent, were used to minimize the impact of potential structural genomic variation on consensus-map quality. The consensus map comprised 3757 unique positions, and the average marker distance was 0.88 cM, obtained by calculating the average distance between two adjacent unique positions. Significant variation of segregation distortion was observed across the three populations. The consensus map was validated by comparing positions of known rust resistance genes, and comparing them to wheat reference genome sequences recently published by the International Wheat Genome Sequencing Consortium, Rye and Ae. tauschii genomes. Three well-characterized rust resistance genes (Sr58/Lr46/Yr29, Sr2/Yr30/Lr27, and Sr57/Lr34/Yr18) and 15 published QTLs for wheat rusts were validated with high resolution. Fifty-two per cent of GBS tags on the consensus map were successfully aligned through BLAST to the right chromosomes on the wheat reference genome sequence.

Conclusion: The consensus map should provide a useful basis for analyzing genome-wide variation of complex traits. The identified genes can then be explored as genetic markers to be used in genomic applications in wheat breeding.

QTL mapping of adult-plant resistance to leaf rust in a RIL population derived from a cross of wheat cultivars Shanghai 3/Catbird and Naxos

Posted by Carelia Juarez on , in Journal Articles

Published in Theoretical and Applied Genetics, 2014

Yue ZhouYan RenLillemo, M.Zhanjun YaoPeipei ZhangXianchun XiaHe Zhonghu;Zaifeng LiDaqun Liu

Leaf rust is an important wheat disease and utilization of adult-plant resistance (APR) may be the best approach to achieve long-term protection from the disease. The CIMMYT spring wheat line Shanghai 3/Catbird (SHA3/CBRD) showed a high level of APR to Chinese Puccinia triticinapathotypes in the field. To identify APR genes in this line, a mapping population of 164 recombinant inbred lines (RILs) was developed from a cross of this line and Naxos, a moderately susceptible German cultivar. The RILs were evaluated for final disease severity (FDS) at Baoding, Hebei province, and Zhoukou, Henan province, in the 2010–2011 and 2011–2012 cropping seasons. QTL analysis detected one major QTL derived from SHA3/CBRD on chromosome 2BS explaining from 15 to 37 % of the phenotypic variance across environments. In addition one minor resistance QTL on chromosome 1AL from SHA3/CBRD and four minor QTL from Naxos on chromosomes 2DL, 5B, 7BS, and 7DS were also detected. SHA3/CBRD also possessed seedling resistance gene Lr26, and Naxos contained Lr1 based on gene postulation following tests with an array of P. triticinapathotypes and molecular marker assays. These seedling resistance and APR genes and their closely linked molecular markers are potentially useful for improving leaf rust resistance in wheat breeding programs.

Mapping quantitative trait loci for pre-harvest sprouting resistance in white-grained winter wheat line CA 0431

Posted by Carelia Juarez on , in Journal Articles

Published in Crop and Pasture Science 64 (6) : 573-579, 2013

Miao, X.L.; Zhang, Y.J.; Xia, X.C.; He Zhonghu; Zhang, Y.; Yan, J.; Chen, X.M.

Pre-harvest sprouting (PHS) in wheat severely reduces yield and end-use quality, resulting in substantial economic losses. The Chinese winter wheat line CA 0431, with white grain, showed high PHS resistance for many years. To identify quantitative trait loci (QTLs) of PHS resistance in this line, 220 F2 plants and the corresponding F2 : 3 lines derived from a cross between CA 0431 and the PHS-susceptible cultivar Zhongyou 206 were used for PHS testing and QTL analysis. Field trials were conducted in Beijing during the 2010–11 and 2011–12 cropping seasons, and in Anyang during 2011–12. PHS resistance was evaluated by assessing the sprouting responses of intact spikes. In total, 1444 molecular markers were used to screen the parents, and 31 markers with polymorphisms between the resistant and susceptible bulks were used to genotype the entire F2 population. Broad-sense heritability of sprouting rate was 0.71 across environments. Inclusive composite interval mapping identified four QTLs, QPhs.caas2BL,QPhs.caas3AS.1QPhs.caas3AS.2, and QPhs.caas3AL, each explaining 2.8–27.7% of the phenotypic variance across environments. The QTLs QPhs.caas3AS.1QPhs.caas3AS.2, and QPhs.caas3AL were located at similar positions to QTLs reported previously, whereas QPhs.caas2BL is likely a new QTL flanked by markers Xbarc1042 andXmag3319. Line CA 0431 and the identified markers can be used in breeding programs targeting improvement of PHS resistance for white-kernel wheat.

Molecular approaches for designing heat tolerant wheat

Posted by Carelia Juarez on , in Journal Articles

Published in Journal of Plant Biochemistry and Biotechnology, 2013

Sundeep Kumar, Prerna Kumari, Uttam Kumar, Monendra Grover, Amit Kumar Singh, Rakesh Singh and R. S. Sengar

Global warming is causing changes in temperature rapidly for over two decades. The increased temperature during reproductive phase of plant growth has emerged as a serious problem all over the world. Constant or transitory high temperatures may affect the plant growth and development which may lead to diverse morphological, physiological and biochemical changes in plants ultimately decrease in yield. Genetic approaches leading to improved thermo-tolerance can mitigate the reduction in yield. In this backdrop, several indirect traits or parameters have been developed for identification of heat tolerant plants/lines. The traits like stay green/delayed senescence are reported to contribute toward capability of plants to tolerate heat stress. In addition, understanding of biochemical and molecular basis of thermo-tolerance in combination with genetic approaches like identification and mapping of heat tolerant QTLs will not only assist conventional breeders to develop heat tolerant cultivars but also help molecular biologists to clone and characterize genes associated with heat tolerance, which could be used in genetically modified heat tolerant plants. Therefore, overviews of different strategies for developing heat tolerant wheat are discussed in this review.

QTL mapping of slow-rusting, adult plant resistance to race Ug99 of stem rust fungus in PBW343/Muu RIL population

Posted by Carelia Juarez on , in Journal Articles

Published in Theoretical and Applied Genetics  126 (5) : 1367-1375, 2013

Sukhwinder Singh, Ravi P. Singh, Sridhar Bhavani, Julio Huerta-Espino and Eric Eugenio Lopez-Vera

Races of stem rust fungus pose a major threat to wheat production worldwide. We mapped adult plant resistance (APR) to Ug99 in 141 lines of a PBW343/Muu recombinant inbred lines (RILs) population by phenotyping them for three seasons at Njoro, Kenya in field trials and genotyping them with Diversity Arrays Technology (DArT) markers. Moderately susceptible parent PBW343 and APR parent Muu displayed mean stem rust severities of 66.6 and 5 %, respectively. The mean disease severity of RILs ranged from 1 to 100 %, with an average of 23.3 %. Variance components for stem rust severity were highly significant (p < 0.001) for RILs and seasons and the heritability (h 2) for the disease ranged between 0.78 and 0.89. Quantitative trait loci (QTL) analysis identified four consistent genomic regions on chromosomes 2BS, 3BS, 5BL, and 7AS; three contributed by Muu (QSr.cim2BS, QSr.cim3BS and QSr.cim7AS) and one (QSr.cim5BL) derived from PBW343. RILs with flanking markers for these QTLs had significantly lower severities than those lacking the markers, and combinations of QTLs had an additive effect, significantly enhancing APR. The QTL identified on chromosome 3BS mapped to the matching region as the known APR gene Sr2. Four additional QTLs on chromosomes 1D, 3A, 4B, and 6A reduced disease severity significantly at least once in three seasons. Our results show a complex nature of APR to stem rust where Sr2 and other minor slow rusting resistance genes can confer a higher level of resistance when present together.

QTL mapping in three tropical maize populations reveals a set of constitutive and adaptive genomic regions for drought tolerance

Posted by Carelia Juarez on , in Journal Articles

Published in Theoretical and Applied Genetics, 2012

Gustavo Dias Almeida, Dan Makumbi, Cosmos Magorokosho, Sudha Nair, Aluízio Borém, Jean-Marcel Ribaut, Marianne Bänziger, Boddupalli M. Prasanna, Jose Crossa and Raman Babu

Despite numerous published reports of quantitative trait loci (QTL) for drought-related traits, practical applications of such QTL in maize improvement are scarce. Identifying QTL of sizeable effects that express more or less uniformly in diverse genetic backgrounds across contrasting water regimes could significantly complement conventional breeding efforts to improve drought tolerance. We evaluated three tropical bi-parental populations under water-stress (WS) and well-watered (WW) regimes in Mexico, Kenya and Zimbabwe to identify genomic regions responsible for grain yield (GY) and anthesis-silking interval (ASI) across multiple environments and diverse genetic backgrounds. Across the three populations, on average, drought stress reduced GY by more than 50 % and increased ASI by 3.2 days. We identified a total of 83 and 62 QTL through individual environment analyses for GY and ASI, respectively. In each population, most QTL consistently showed up in each water regime. Across the three populations, the phenotypic variance explained by various individual QTL ranged from 2.6 to 17.8 % for GY and 1.7 to 17.8 % for ASI under WS environments and from 5 to 19.5 % for GY under WW environments. Meta-QTL (mQTL) analysis across the three populations and multiple environments identified seven genomic regions for GY and one for ASI, of which six mQTL on chr.1, 4, 5 and 10 for GY were constitutively expressed across WS and WW environments. One mQTL on chr.7 for GY and one on chr.3 for ASI were found to be ‘adaptive’ to WS conditions. High throughput assays were developed for SNPs that delimit the physical intervals of these mQTL. At most of the QTL, almost equal number of favorable alleles was donated by either of the parents within each cross, thereby demonstrating the potential of drought tolerant × drought tolerant crosses to identify QTL under contrasting water regimes.


QTL mapping of adult-plant resistance to stripe rust in a population derived from common wheat cultivars Naxos and Shanghai 3/Catbird

Posted by Carelia Juarez on , in Journal Articles

Published in Theoretical and Applied Genetics, 2012

Yan Ren, Zhonghu He, Jia Li, Morten Lillemo, Ling Wu, Bin Bai, Qiongxian Lu, Huazhong Zhu, Gang Zhou and Jiuyuan Du, et al.

Stripe rust, caused by Puccinia striiformis Westend. f. sp. tritici Erikss., is a severe foliar disease of common wheat (Triticum aestivum L.) worldwide. Use of adult-plant resistance (APR) is an efficient approach to provide long-term protection of crops from the disease. The German spring wheat cultivar Naxos showed a high level of APR to stripe rust in the field. To identify the APR genes in this cultivar, a mapping population of 166 recombinant inbred lines (RILs) was developed from a cross between Naxos and Shanghai 3/Catbird (SHA3/CBRD), a moderately susceptible line developed by CIMMYT. The RILs were evaluated for maximum disease severity (MDS) in Sichuan and Gansu in the 2009–2010 and 2010–2011 cropping seasons. Composite interval mapping (CIM) identified four QTL, QYr.caas1BL.1RS, QYr.caas1DS, QYr.caas5BL.3 and QYr.caas7BL.1, conferring stable resistance to stripe rust across all environments, each explaining 1.9–27.6, 2.1–5.8, 2.5–7.8 and 3.7–9.1 % of the phenotypic variance, respectively. QYr.caas1DS flanked by molecular markers XUgwm353Xgdm33b was likely a new QTL for APR to stripe rust. Because the interval between flanking markers for each QTL was less than 6.5 cM, these QTL and their closely linked markers are potentially useful for improving resistance to stripe rust in wheat breeding.

QTL mapping of adult-plant resistances to stripe rust and leaf rust in Chinese wheat cultivar Bainong 64

Posted by Carelia Juarez on , in Journal Articles

Published in Theoretical and Applied Genetics, 2012

Yan Ren, Zaifeng Li, Zhonghu He, Ling Wu, Bin Bai, Caixia Lan, Cuifen Wang, Gang Zhou, Huazhong Zhu and Xianchun Xia

Stripe rust and leaf rust, caused by Puccinia striiformis Westend. f. sp. tritici Erikss. and P. triticina, respectively, are devastating fungal diseases of common wheat (Triticum aestivum L.). Chinese wheat cultivar Bainong 64 has maintained acceptable adult-plant resistance (APR) to stripe rust, leaf rust and powdery mildew for more than 10 years. The aim of this study was to identify quantitative trait loci/locus (QTL) for resistance to the two rusts in a population of 179 doubled haploid (DH) lines derived from Bainong 64 × Jingshuang 16. The DH lines were planted in randomized complete blocks with three replicates at four locations. Stripe rust tests were conducted using a mixture of currently prevalent P. striiformis races, and leaf rust tests were performed with P. triticina race THTT. Leaf rust severities were scored two or three times, whereas maximum disease severities (MDS) were recorded for stripe rust. Using bulked segregant analysis (BSA) and simple sequence repeat (SSR) markers, five independent loci for APR to two rusts were detected. The QTL on chromosomes 1BL and 6BS contributed by Bainong 64 conferred resistance to both diseases. The loci identified on chromosomes 7AS and 4DL had minor effects on stripe rust response, whereas another locus, close to the centromere on chromosome 6BS, had a significant effect only on leaf rust response. The loci located on chromosomes 1BL and 4DL also had significant effects on powdery mildew response. These were located at the same positions as the Yr29/Lr46 and Yr46/Lr67 genes, respectively. The multiple disease resistance locus for APR on chromosome 6BS appears to be new. All three genes and their closely linked molecular markers could be used in breeding wheat cultivars with durable resistance to multiple diseases.

Computer simulation in plant breeding

Posted by Carelia Juarez on , in Journal Articles

Published in Advances in Agronomy 116: 219-264, 2012

Xin Li, Chengsong Zhu, Jiankang Wang and Jianming Yu

As a bridge between theory and experimentation, computer simulation has become a powerful tool in scientific research, providing not only preliminary validation of theories but also guidelines for empirical experiments. Plant breeding focuses on developing superior genotypes with available genetic and nongenetic resources, and improved plant-breeding methods maximize genetic gain and cost-effectiveness. Computer simulation can lay out the breeding process in silico and identify optimal candidates for various scenarios; empirical validation can then follow. Insights gained from empirical studies, in turn, can be incorporated into computer simulations. In this review, we discuss different applications of computer simulation in plant breeding. First, we briefly summarize the history of plant breeding and computer simulation and how computer simulation can facilitate the breeding process. Next, we partition the utility of computer simulation into different research areas of plant breeding, including breeding method comparison, genetic mapping, gene network and genotype-by-environment interaction simulation, and crop modeling. Then we discuss computational issues involved in simulation. Finally, we offer some perspectives on the future of computer simulation in plant breeding.

QTL mapping of terminal heat tolerance in hexaploid wheat (T. aestivum L.)

Posted by Carelia Juarez on , in Journal Articles

Published in Theoretical and Applied Genetics 125 (3): 561-575, 2012

Rajneesh Paliwal, Marion S. Röder, Uttam Kumar, J. P. Srivastava and Arun Kumar Joshi

High temperature (>30 °C) at the time of grain filling is one of the major causes of yield reduction in wheat in many parts of the world, especially in tropical countries. To identify quantitative trait loci (QTL) for heat tolerance under terminal heat stress, a set of 148 recombinant inbred lines was developed by crossing a heat-tolerant hexaploid wheat (Triticum aestivum L.) cultivar (NW1014) and a heat-susceptible (HUW468) cultivar. The F5, F6, and F7 generations were evaluated in two different sowing dates under field conditions for 2 years. Using the trait values from controlled and stressed trials, four different traits (1) heat susceptibility index (HSI) of thousand grain weight (HSITGW); (2) HSI of grain fill duration (HSIGFD); (3) HSI of grain yield (HSIYLD); and (4) canopy temperature depression (CTD) were used to determine heat tolerance. Days to maturity was also investigated. A linkage map comprising 160 simple sequence repeat markers was prepared covering the whole genome of wheat. Using composite interval mapping, significant genomic regions on 2B, 7B and 7D were found to be associated with heat tolerance. Of these, two (2B and 7B) were co-localized QTL and explained more than 15 % phenotypic variation for HSITGW, HSIGFD and CTD. In pooled analysis over three trials, QTL explained phenotypic variation ranging from 9.78 to 20.34 %. No QTL × trial interaction was detected for the identified QTL. The three major QTL obtained can be used in marker-assisted selection for heat stress in wheat.