Posts Tagged ‘Molecular Breeding’

Genetic relationships and structure among open-pollinated maize varieties adapted to eastern and southern Africa using microsatellite markers

Posted by Carelia Juarez on , in Journal Articles

Published in Molecular Breeding, 2014

Fentaye Kassa SemagnMagorokosho, C.Ogugo, V.Makumbi, D.Warburton, M.L.

Molecular characterization of open-pollinated maize varieties (OPVs) is fundamentally important in maize germplasm improvement. We investigated the extent of genetic differences, patterns of relationships, and population structure among 218 diverse OPVs widely used in southern and eastern Africa using the model-based population structure, analysis of molecular variance, cluster analysis, principal component analysis, and discriminant analysis. The OPVs were genotyped with 51 microsatellite markers and the fluorescent detection system of the Applied Biosystems 3730 Capillary Sequencer. The number of alleles detected in each OPV varied from 72 to 155, with an overall mean of 127.6. Genetic distance among the OPVs varied from 0.051 to 0.434, with a mean of 0.227. The different multivariate methods suggest the presence of 2–4 possible groups, primarily by maturity groups but also with overlapping variation between breeding programs, mega-environments, and specific agronomic traits. Nearly all OPVs in group 1 and group 2 belong to the intermediate-late and early maturity groups, respectively. Group 3 consisted of mainly intermediate maturing OPVs, while group 4 contained OPVs of different maturity groups. The OPVs widely used in eastern Africa either originated from the southern African maize breeding programs, or the majority of inbred lines used as parents by the two breeding programs in developing the OPVs might be genetically related. Some of the OPVs are much older than others, but they still did not show a clear pattern of genetic differentiation as compared with the recently developed ones, which is most likely due to recycling of the best parental lines in forming new OPVs.

QTL characterization of resistance to leaf rust and stripe rust in the spring wheat line Francolin#1

Posted by Carelia Juarez on , in Journal Articles

Published in Molecular Breeding, 2014

Caixia Lan;Rosewarne, G.M.; Singh, R.P.; Herrera-Foessel, S.A.; Huerta-Espino, J.; Basnet, B.R.; Yelun Zhang; Ennian Yang.

Growing resistant wheat varieties is a key method of controlling two important wheat diseases, leaf rust and stripe rust. We analyzed quantitative trait loci (QTL) to investigate adult plant resistance (APR) to these rusts, using 141 F5 RILs derived from the cross ‘Avocet-YrA/Francolin#1’. Phenotyping of leaf rust resistance was conducted during two seasons at Ciudad Obregon, Mexico, whereas stripe rust was evaluated for two seasons in Toluca, Mexico, and one season in Chengdu, China. The genetic map was constructed with 581 markers, including diversity arrays technology and simple sequence repeat. Significant loci for reducing leaf rust severity were designated QLr.cim1BLQLr.cim3BS.1QLr.cim3DC, and QLr.cim7DS. The six QTL that reduced stripe rust severity were designated QYr.cim1BLQYr.cim2BSQYr.cim2DSQYr.cim3BS.2QYr.cim5AL, andQYr.cim6AL. All loci were conferred by Francolin#1, with the exception of QYr.cim2DSQYr.cim5AL, and QYr.cim6AL, which were derived from Avocet-YrA. Closely linked markers indicated that the 1BL locus was the pleiotropic APR gene Lr46/Yr29QYr.cim2BS was a seedling resistance gene designated as YrF that conferred intermediate seedling reactions and moderate resistance at the adult plant stage in both Mexican and Chinese environments. Significant additive interactions were detected between the six QTL for stripe rust, but not between the four QTL for leaf rust. Furthermore, we detected two new APR loci for leaf rust in common wheat: QLr.cim3BS.1 andQLr.cim7DS.

Molecular mapping across three populations reveals a QTL hotspot region on chromosome 3 for secondary traits associated with drought tolerance in tropical maize

Posted by Carelia Juarez on , in Journal Articles

Published in Molecular Breeding, 2014

Dias Almeida, G.; Nair, S.; Borem, A.; Cairns, J.; Trachsel, S.;Ribaut, J-M; Banziger, M.; Prasanna, B.M.; Crossa, J.; Babu, R.

Identifying quantitative trait loci (QTL) of sizeable effects that are expressed in diverse genetic backgrounds across contrasting water regimes particularly for secondary traits can significantly complement the conventional drought tolerance breeding efforts. We evaluated three tropical maize biparental populations under water-stressed and well-watered regimes for drought-related morpho-physiological traits, such as anthesis-silking interval (ASI), ears per plant (EPP), stay-green (SG) and plant-to-ear height ratio (PEH). In general, drought stress reduced the genetic variance of grain yield (GY), while that of morpho-physiological traits remained stable or even increased under drought conditions. We detected consistent genomic regions across different genetic backgrounds that could be target regions for marker-assisted introgression for drought tolerance in maize. A total of 203 QTL for ASI, EPP, SG and PEH were identified under both the water regimes. Meta-QTL analysis across the three populations identified six constitutive genomic regions with a minimum of two overlapping traits. Clusters of QTL were observed on chromosomes 1.06, 3.06, 4.09, 5.05, 7.03 and 10.04/06. Interestingly, a ~8-Mb region delimited in 3.06 harboured QTL for most of the morpho-physiological traits considered in the current study. This region contained two important candidate genes viz., zmm16 (MADS-domain transcription factor) and psbs1 (photosystem II unit) that are responsible for reproductive organ development and photosynthate accumulation, respectively. The genomic regions identified in this study partially explained the association of secondary traits with GY. Flanking single nucleotide polymorphism markers reported herein may be useful in marker-assisted introgression of drought tolerance in tropical maize.

Molecular mapping of leaf rust resistance gene LrFun in Romanian wheat line Fundulea 900

Posted by Carelia Juarez on , in Journal Articles

Published in Molecular Breeding, 2013

Lifang Xing; Cuifen Wang; Xianchun Xia; He Zhonghu; Wanquan Chen; Taiguo Liu; Zaifeng Li; Daqun Liu

Leaf rust, caused by Puccinia triticina, is one of the major wheat diseases worldwide and poses a constant threat to common wheat (Triticum aestivum L.) production and food security. Results from the F2 and F2:3 populations derived from a cross between resistant line Fundulea 900 and susceptible cultivar Thatcher indicated that a single dominant gene, tentatively designated LrFun,conferred resistance to leaf rust. In order to identify other possible genes in Fundulea 900, nine P.triticina pathotypes avirulent on Fundulea 900 were used to inoculate F2:3 families. The results showed that at least two leaf rust resistance genes were present in Fundulea 900. A total of 1,706 pairs of simple sequence repeat (SSR) primers were used to test the parents and resistant and susceptible bulks. Eight polymorphic markers from chromosome 7BL were used for genotyping the F2 and F2:3 populations. LrFun was linked to eight SSR loci on chromosome 7BL. The two closest flanking SSR loci were Xgwm344 and Xwmc70, with genetic distances of 4.4 and 5.7 cM, respectively. At present four leaf rust resistance genes, Lr14aLr14bLr68 and LrBi16, are located on chromosome 7BL. In a seedling test with 12 P. triticina isolates, the reaction patterns of LrFunwere different from those of lines carrying Lr14aLr14b and LrBi16Lr68 is an adult plant resistance gene, and it is different from the seedling resistance gene LrFun. Therefore, we concluded that LrFunis a new leaf rust resistance gene.

Characterization of Yr54 and other genes associated with adult plant resistance to yellow rust and leaf rust in common wheat Quaiu 3

Posted by Carelia Juarez on , in Journal Articles

Published in Molecular Breeding, 2013

Basnet, B.R.; Singh, R.P.; Ibrahim, A.M.H.; Herrera-Foessel, S.A.; Huerta-Espino, J.; Lan, C.; Rudd, J.C.

Leaf rust (LR) and yellow rust (YR), caused by Puccinia triticina and Puccinia striiformis f. sp. tritici, respectively, are important diseases of wheat. Quaiu 3, a common wheat line developed at the International Maize and Wheat Improvement Center (CIMMYT), is immune to YR in Mexico despite seedling susceptibility to predominant races. Quaiu 3 also shows immunity to LR in field trials and is known to possess the race-specific gene Lr42. A mapping population of 182 recombinant inbred lines (RILs) was developed by crossing Quaiu 3 with susceptible Avocet-YrA and phenotyped with LR and YR in field trials for 2 years in Mexico. Quantitative trait loci (QTL) associated with YR and LR resistance in the RILs were identified using Diversity Arrays Technology and simple sequence repeat markers. A large-effect QTL on the long arm of chromosome 2D explained 49–54 % of the phenotypic variation in Quaiu 3 and was designated as Yr54. Two additional loci on 1BL and 3BS explained 8–17 % of the phenotypic variation for YR and coincided with previously characterized adult plant resistance (APR) genes Lr46/Yr29 and Sr2/Yr30, respectively. QTL on 1DS and 1BL corresponding to Lr42 and Lr46/Yr29, respectively, contributed 60–71 % of the variation for LR resistance. A locus on 3D associated with APR to both diseases explained up to 7 % of the phenotypic variance. Additional Avocet-YrA-derived minor QTL were also detected for YR on chromosomes 1A, 3D, 4A, and 6A. Yr54 is a newly characterized APR gene which can be combined with other genes by using closely linked molecular markers.

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.

Single nucleotide polymorphism genotyping using Kompetitive Allele Specific PCR (KASP): overview of the technology and its application in crop improvement

Posted by Carelia Juarez on , in Journal Articles

Published in Molecular Breeding, 2013

Kassa Semagn, Raman Babu, Sarah Hearne and Michael Olsen

Single nucleotide polymorphism (SNP) data can be obtained using one of the numerous uniplex or multiplex SNP genotyping platforms that combine a variety of chemistries, detection methods, and reaction formats. Kompetitive Allele Specific PCR (KASP) is one of the uniplex SNP genotyping platforms, and has evolved to be a global benchmark technology. However, there are no publications relating either to the technology itself or to its application in crop improvement programs. In this review, we provide an overview of the different aspects of the KASP genotyping platform, discuss its application in crop improvement, and compare it with the chip-based Illumina GoldenGate platform. The International Maize and Wheat Improvement Center routinely uses KASP, generating in excess of a million data points annually for crop improvement purposes. We found that (1) 81 % of the SNPs used in a custom-designed GoldenGate assay were transferable to KASP; (2) using KASP, negative controls (no template) consistently clustered together and rarely produced signals exceeding the threshold values for allele calling, in contrast to the situation observed using GoldenGate assays; (3) KASP’s average genotyping error in positive control DNA samples was 0.7–1.6 %, which is lower than that observed using GoldenGate (2.0–2.4 %); (4) KASP genotyping costs for marker-assisted recurrent selection were 7.9–46.1 % cheaper than those of the BeadXpress and GoldenGate platforms; and (5) KASP offers cost-effective and scalable flexibility in applications that require small to moderate numbers of markers, such as quality control analysis, quantitative trait loci (QTL) mapping in bi-parental populations, marker-assisted recurrent selection, marker-assisted backcrossing, and QTL fine mapping.

Genetics of resistance to yellow rust in PBW343 × Kenya Kudu recombinant inbred line population and mapping of a new resistance gene YrKK

Posted by Carelia Juarez on , in Journal Articles

Published in Molecular Breeding, 2013

Zaifeng Li, Sukhwinder Singh, Ravi P. Singh, Eric E. López-Vera and  Julio Huerta-Espino

Yellow or stripe rust, caused by Puccinia striiformis f. sp. tritici, is an important disease of common wheat (Triticum aestivum L.) worldwide. A recombinant inbred line (RIL) population, derived from the cross PBW343 × Kenya Kudu, was phenotyped for yellow rust reaction in the field at the CIMMYT research station near Toluca, Mexico, during 2010 and 2011. Segregation results indicated the presence of a race-specific resistance gene, temporarily designated as YrKK, in Kenya Kudu that conferred immunity to adult plants in field trials, despite conferring only slight reductions in seedling reactions in greenhouse tests with three Mexican pathotypes. A minimum of four minor genes having additive effects also segregated in the population and were likely derived from both parents. A total of 635 simple sequence repeat (SSR) primers were screened for polymorphism surveys on the parents, and resistant (YrKK-possessing RILs) and susceptible (YrKK-lacking RILs) bulks identified four polymorphic markers. These markers were located on the short arm of chromosome 2B. Genotypingof the entire RIL population identified Xgwm148 and Xwmc474 as the most closely linked proximal and distal flanking SSR markers, with respective genetic distances of 3.6 and 1.8 cM from YrKK. Four yellow rust resistance genes (Yr27Yr31Yr41, and YrP81) are located on chromosome 2BS; however, their specificity to pathogen pathotypes and host reactions in seedling and adult plants indicate that YrKK is a new resistance gene.

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.

Identification and mapping of leaf, stem and stripe rust resistance quantitative trait loci and their interactions in durum wheat

Posted by Carelia Juarez on , in Journal Articles

Published in Molecular Breeding, 2012

A. Singh, M. P. Pandey, A. K. Singh, R. E. Knox, K. Ammar, J. M. Clarke, F. R. Clarke, R. P. Singh, C. J. Pozniak, R. M. DePauw, B. D. McCallum, R. D. Cuthbert, H. S. Randhawa and T. G. Fetch Jr.

Leaf rust (Puccinia triticina Eriks.), stripe rust (Puccinia striiformis f. tritici Eriks.) and stem rust (Puccinia graminis f. sp. tritici) cause major production losses in durum wheat (Triticum turgidum L. var. durum). The objective of this research was to identify and map leaf, stripe and stem rust resistance loci from the French cultivar Sachem and Canadian cultivar Strongfield. A doubled haploid population from Sachem/Strongfield and parents were phenotyped for seedling reaction to leaf rust races BBG/BN and BBG/BP and adult plant response was determined in three field rust nurseries near El Batan, Obregon and Toluca, Mexico. Stripe rust response was recorded in 2009 and 2011 nurseries near Toluca and near Njoro, Kenya in 2010. Response to stem rust was recorded in field nurseries near Njoro, Kenya, in 2010 and 2011. Sachem was resistant to leaf, stripe and stem rust. A major leaf rust quantitative trait locus (QTL) was identified on chromosome 7B at Xgwm146 in Sachem. In the same region on 7B, a stripe rust QTL was identified in Strongfield. Leaf and stripe rust QTL around DArT marker wPt3451 were identified on chromosome 1B. On chromosome 2B, a significant leaf rust QTL was detected conferred by Strongfield, and at the same QTL, a Yr gene derived from Sachem conferred resistance. Significant stem rust resistance QTL were detected on chromosome 4B. Consistent interactions among loci for resistance to each rust type across nurseries were detected, especially for leaf rust QTL on 7B. Sachem and Strongfield offer useful sources of rust resistance genes for durum rust breeding.