Posts Tagged ‘Molecular markers’

Fine mapping of leaf rust resistance gene Lrzh84 using expressed sequence tag and sequence-tagged site markers, and allelism with other genes on wheat chromosome 1b

Posted by Carelia Juarez on , in Journal Articles

Published in Phytopathology 103 (2) : 169-174, 2013

Yue Zhou; Xianchun Xia; He Zhonghu; Xing Li;Zaifeng Li; Daqun Liu

Zhou 8425B, possessing the leaf rust resistance gene LrZH84, is an elite wheat (Triticum aestivum) parental line in the Yellow-Huai Valley region of China. In the present study, 2,086 F2 plants derived from Zhou 8425B/Chinese Spring were used for fine mapping of LrZH84 with expressed sequence tag (EST) and sequence-tagged site (STS) markers. Seventy inter-simple sequence repeat EST and STS markers on 1BL were used to screen the two parents and resistant and susceptible bulks; those polymorphic were used to analyze the entire F2 population. Three EST markers (BF474863, BE497107, and CD373538) were closely linked to LrZH84, with genetic distances of 0.7, 0.7, and 1.7 cM, respectively. STS marker Hbsf-1 was developed from the sequences of polymerase chain reaction fragments amplified from EST marker BF474863. LrZH84 was 8.19 cM proximal to Lr44, but may be allelic to LrXi and LrG98 although they showed different reactions with some Puccinia triticina pathotypes.

Formation of heterotic groups and understanding genetic effects in a provitamin a biofortified maize breeding program

Posted by Carelia Juarez on , in Journal Articles

Published in Crop Science, 2013

Willy B. Suwarno, Kevin V. Pixley, Natalia Palacios-Rojas, Shawn M. Kaeppler and Raman Babu

Developing biofortified maize cultivars is a viable approach to combat the widespreadproblem of vitamin A deficiency among people for whom maize is a staple food. To enhance CIMMYT?s provitamin A maize breeding efforts, this study: 1) evaluated whether separation of experimental maize lines into groups based on maximizing their molecular-marker-based genetic distances (GD) resulted in heterosis for among-group crosses, 2) assessed genetic effects (general and specific combining ability, GCA and SCA) for grain yield and provitamin A concentrations in hybrids among 21 inbred lines representing the three proposed groups, and 3) assessed the association between grain yield and provitamin A concentrations. The lines were crossed following a partial diallel design resulting in 156 hybrids which were evaluated at four environments with two replications of one-row plots. The first plant in each plot was self-pollinated to produce grain for provitamin A analysis. Significant but small yield advantage of among versus within group crosses (0.47 Mg ha-1 21 , P<0.05) suggested that the groups identified by maximizing GD could be a practicalstarting point for further breeding work to develop useful heterotic groups. Furthermore, the GD-proposed heterotic groups were improved by later revising some line assignments to groups using estimates of SCA effects. GCA effects were significant (P<0.01) for all traits, whereas SCA effects were weak (P<0.05) or not significant for provitamin A carotenoid concentrations, indicating that these were controlled primarily by additive gene action. Grain yield was not significantly correlated with provitamin A concentration, indicating that both traits could be improved simultaneously.

Fine mapping of leaf rust resistance Genelrzh84 using expressed sequence tag and sequence-tagged site markers, and Allelism with other genes on wheat chromosome 1B

Posted by Carelia Juarez on , in Journal Articles

Published in Phytopathology 103 (2) : 169-174, 2013

Yue Zhou, Xianchun Xia, Zhonghu He, Xing Li, Zaifeng Li and Daqun Liu

Zhou 8425B, possessing the leaf rust resistance gene LrZH84, is an  elite wheat (Triticum aestivum) parental line in the Yellow-Huai Valley  region of China. In the present study, 2,086 F2  plants derived from Zhou 8425B/Chinese Spring were used for fine mapping of LrZH84 with expressed sequence tag (EST) and sequence-tagged site (STS) markers. Seventy inter-simple sequence repeat EST and STS markers on 1BL were used to screen the two parents and resistant and susceptible bulks; those polymorphic were used to analyze the entire F2 population. Three EST markers (BF474863, BE497107, and CD373538) were closely linked to LrZH84, with genetic distances of 0.7, 0.7, and 1.7 cM, respectively. STS marker Hbsf-1 was developed from the sequences of polymerase chain reaction fragments amplified from EST marker BF474863. LrZH84 was 8.19 cM proximal to Lr44, but may be allelic to LrXi and LrG98 although they showed different reactions with some Puccinia triticina pathotypes.

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.

Pyramiding adult-plant powdery mildew resistance QTLs in bread wheat

Posted by Carelia Juarez on , in Journal Articles

Published in Crop and Pasture Science 63 (7) : 606-611, 2012

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

Pyramiding of quantitative trait loci (QTLs) can be an effective approach for developing durable resistance to powdery mildew in wheat (Triticum aestivum L.). The Chinese wheat cultivars Bainong 64 and Lumai 21, with outstanding agronomic traits, possess four and three QTLs, respectively, for adult-plant resistance (APR) to powdery mildew. To achieve optimal durable resistance, 21 F6 lines combining two–five powdery mildew APR QTLs were developed from the cross Bainong 64/Lumai 21 using a modified pedigree selection. These lines were planted in a randomised complete block design with two replicates in Beijing during the 2009–10 and 2010–11 cropping seasons, and were evaluated for powdery mildew response using the highly virulent Blumeria graminis f. sp. tritici isolate E20. Based on the phenotypic data of both maximum disease severity (MDS) and area under the disease progress curve (AUDPC), analysis of variance indicated that there were highly significant effects of QTL combinations on reducing powdery mildew MDS and AUDPC. Six pyramided QTL combinations possessing QPm.caas1A and QPm.caas4DL in common along with one or more of the others expressed better APR to powdery mildew than the more resistant parent, Bainong 64. Thus, pyramiding these two QTLs with one or more of QPm.caas2BS, QPm.caas2BL, and QPm.caas2DL from Lumai 21 could be a desirable strategy to breed cultivars with high levels of durable resistance to powdery mildew. Experienced breeders with a good knowledge of minor genes can achieve APR by phenotypic selection, and selection by molecular markers will still require uniform field testing for powdery mildew and disease phenotype to validate the resistance. These results provided very useful information for pyramiding APR QTLs in wheat breeding programs.

The screening of wheat germplasm for resistance to stripe and leaf rust in Kazakhstan using molecular markers

Posted by Carelia Juarez on , in Journal Articles

Published in Journal of Life Sciences 6 (9) : 353-362, 2012

A. Kokhmetova, G. Yessenbekova, A.I. Morgounov and F. Ogbonnaya

Resistance to stripe and leaf rusts is the most important objectives in Kazakhstan, and they are the major factor that adversely affects wheat yield and quality and finally causes considerable economic damage. This study was aimed at characterizing elite wheat germplasm from Central Asia using molecular markers linked to the Lr34/Yr18 dual rust resistance gene and to identify new wheat germplasm resistant to leaf and yellow rust. In experiment with germplasm developed from Kazakhstan and Central and West Asia yellow rust trap nursery (CIMMYT), the frequency of the csLV34b-allele linked to Lr34/Yr18 (150 bp) was low and only seven of the 42 accessions had allele diagnostic of Lr34/Yr18. Two genotypes had high level of resistance, showing immune reaction to all three rusts. Disease severity from resistance to moderate susceptible was recorded in the lines having Lr34/Yr18 genes, which is comparable to the disease severity observed on the cultivar, Cook (20MS-30MS), carrying Lr34/Yr18 genes. The molecular screening of a set of additional 51 wheat genotypes, including commercial cultivars and breeding lines from different countries, showed that the csLV34 marker was present in 20 genotypes. This allowed us to select lines that could be used for future breeding work. In all, a total of 269 lines possessed effective Lr34/Yr18 gene complex: 28 lines of F4 Almaly/Opata-85, 34 lines of Almaly/Super Kauz, 26 lines of F4 Parula/(Almaly/Anza), 23 lines of F4 Babax 1/Opata 85, and 27 lines of Madsen/Cook populations. This further validates and confirms that the STS marker csLV34 and morphological marker leaf tip necrosis are reliable in the identification of carriers of effective slow rusting Lr34/Yr18 gene. The germplasms identified are further being tested for end-used quality and could be released by NARS as varieties in the various countries of Central Asia.

Validation of the effects of molecular marker polymorphisms in LcyE and CrtRB1 on provitamin A concentrations for 26 tropical maize populations

Posted by Carelia Juarez on , in Journal Articles

Published in Theoretical and Applied Genetics, 2012

Raman Babu, Natalia Palacios Rojas, Shibin Gao, Jianbing Yan and Kevin Pixley

Vitamin A deficiency (VAD) compromises immune function and is the leading cause of preventable blindness in children in many developing countries. Biofortification, or breeding staple food crops that are rich in micronutrients, provides a sustainable way to fight VAD and other micronutrient malnutrition problems. Polymorphisms, with associated molecular markers, have recently been identified for two loci, LcyE (lycopene epsilon cyclase) and CrtRB1 (β-carotene hydroxylase 1) that govern critical steps in the carotenoid biosynthetic pathway in maize endosperm, thereby enabling the opportunity to integrate marker-assisted selection (MAS) into carotenoid breeding programs. We validated the effects of 3 polymorphisms (LcyE5′TE, LcyE3′Indel and CrtRB1-3′TE) in 26 diverse tropical genetic backgrounds. CrtRB1-3′TE had a two-ten fold effect on enhancing beta-carotene (BC) and total provitamin A (proA) content. Reduced-function, favorable polymorphisms within LcyE resulted in 0–30 % reduction in the ratio of alpha- to beta-branch carotenoids, and increase in proA content (sometimes statistically significant). CrtRB1-3′TE had large, significant effect on enhancing BC and total ProA content, irrespective of genetic constitution for LcyE5′TE. Genotypes with homozygous favorable CrtRB1-3′TE alleles had much less zeaxanthin and an average of 25 % less total carotenoid than other genotypes, suggesting that feedback inhibition may be reducing the total flux into the carotenoid pathway. Because this feedback inhibition was most pronounced in the homozygous favorable LcyE (reduced-function) genotypes, and because maximum total proA concentrations were achieved in genotypes with homozygous unfavorable or heterozygous LcyE, we recommend not selecting for both reduced-function genes in breeding programs. LcyE exhibited significant segregation distortion (SD) in all the eight, while CrtRB1 in five of eight digenic populations studied, with favorable alleles of both the genes frequently under-represented. MAS using markers reported herein can efficiently increase proA carotenoid concentration in maize.

 

Genome-enabled prediction of genetic values using radial basis function neural networks

Posted by Carelia Juarez on , in Journal Articles

Published in Theoretical and Applied Genetics 125 (4): 759-771, 2012

J. M. González-Camacho, G. de los Campos, P. Pérez, D. Gianola, J. E. Cairns, G. Mahuku, R. Babu and J. Crossa

The availability of high density panels of molecular markers has prompted the adoption of genomic selection (GS) methods in animal and plant breeding. In GS, parametric, semi-parametric and non-parametric regressions models are used for predicting quantitative traits. This article shows how to use neural networks with radial basis functions (RBFs) for prediction with dense molecular markers. We illustrate the use of the linear Bayesian LASSO regression model and of two non-linear regression models, reproducing kernel Hilbert spaces (RKHS) regression and radial basis function neural networks (RBFNN) on simulated data and real maize lines genotyped with 55,000 markers and evaluated for several trait–environment combinations. The empirical results of this study indicated that the three models showed similar overall prediction accuracy, with a slight and consistent superiority of RKHS and RBFNN over the additive Bayesian LASSO model. Results from the simulated data indicate that RKHS and RBFNN models captured epistatic effects; however, adding non-signal (redundant) predictors (interaction between markers) can adversely affect the predictive accuracy of the non-linear regression models.

Distribution of Allelic variation for vernalization, photoperiod, and dwarfing genes and their effects on growth period and plant height among cultivars from major wheat producing countries

Posted by Carelia Juarez on , in Journal Articles

Published in Acta Agronomica Sinica, 2012

Yang Fang-Ping, Xia Xian-Chun, Zhang Yong, Zhang Xiao-ke,  Liu Jian-Jun, Tang Jian-Wei, Yang Xue-Ming, Zhang Jun-Ru, Liu Qian, Li Shi-zhao, and He Zhonghu

To efficiently use exotic resources in Chinese wheat breeding programs, we investigated the heading date, maturity date, and plant height of 100 representative cultivars collected from 14 countries at eight locations in China, and detected the allelic variations of vernalization loci VRN-1 and VRN-B3, photoperiod gene Ppd-D1a,and dwarfing genes Rht-B1b and Rht-D1b by means of molecular markers. The frequencies of vernalization loci were 8.0% for Vrn-A1a, 21.0% for Vrn-B1, 21.0% for Vrn-D1 and 64.0% for vrn-A1+vrn-B1+ vrn-D1, except for the absence of dominant allele Vrn-B3 in all tested materials. Dominant vernalization alleles Vrn-A1a, Vrn-B1, and Vrn-D1 were mainly observed in cultivars from Chinese spring wheat region, Italy, India, Canada, Mexico, and Australia; whereas, cultivars carrying all recessive alleles at the four vernalization loci and vrn-A1+vrn-D1+Vrn-B1+vrn-B3 genotypewere mostly found in cultivars from Chinese winter wheat region, United States (US) winter wheat region, Russia winter wheat region, United Kingdom (UK), France, Germany, Romania, Turkey, and Hungary. All cultivars headed normally when sown in autumn. Cultivars with dominant alleles showed earlier heading date than those with recessive alleles, and genotypes with two or more dominant alleles showed additive effects. Some European and US cultivars with recessive genes at the four vernalization loci could not mature in Yangling and Chengdu. Under spring-sown condition, the cultivars with dominant vernalization alleles showed high heading frequency; in contrast, most cultivars with recessive alleles failed to head. Gene Ppd-D1a was distributed mainly in cultivars from China, France, Romania, Russia, Mexico, Australia, and India with the total frequency of 68%. Most cultivars with Ppd-D1b were from high latitude regions, such as UK, Germany, Hungary, and Canada. The Ppd-D1a genotypes appeared to head earlier than the Ppd-D1b genotypes. Daylight condition had no effect on maturity of most Ppd-D1a genotypes, but short daylight condition resulted in failing mature in most Ppd-D1b genotypes. The frequencies of dwarfing genes Rht-B1b and Rht-D1b were 43.0% and 35.0% in the cultivars tested, respectively. Rht-B1b was mainly observed in cultivars from US, Romania, Turkey, Italy, Mexico, and Australia, while Rht-D1b had high frequency in varieties from China, Germany, UK, Italy, and India. Generally, cultivars from one country contain either Rht-B1b or Rht-D1b, andthe frequencies of Rht-B1b and Rht-D1b were very low in cultivars from high latitude regions. The effect of Rht-B1b, Rht-D1b and Ppd-D1a on reducing plant height was significant, of which Rht-B1b and Rht-D1b exhibited an additive effect.

 

Molecular characterization of diverse CIMMYT maize inbred lines from eastern and southern Africa using single nucleotide polymorphic markers

Posted by Carelia Juarez on , in Journal Articles

Published in BMC Genomics 13: 113, 2012

Kassa Semagn, Cosmos Magorokosho, Bindiganavile S Vivek, Dan Makumbi, Yoseph Beyene, Stephen Mugo, BM Prasanna and Marilyn L Warburton

Background

 Knowledge of germplasm diversity and relationships among elite breeding materials is fundamentally important in crop improvement. We genotyped 450 maize inbred lines developed and/or widely used by CIMMYT breeding programs in both Kenya and Zimbabwe using 1065 SNP markers to (i) investigate population structure and patterns of relationship of the germplasm for better exploitation in breeding programs; (ii) assess the usefulness of SNPs for identifying heterotic groups commonly used by CIMMYT breeding programs; and (iii) identify a subset of highly informative SNP markers for routine and low cost genotyping of CIMMYT germplasm in the region using uniplex assays.

 Results

 Genetic distance for about 94% of the pairs of lines fell between 0.300 and 0.400. Eighty four percent of the pairs of lines also showed relative kinship values ≤ 0.500. Model-based population structure analysis, principal component analysis, neighbor-joining cluster analysis and discriminant analysis revealed the presence of 3 major groups and generally agree with pedigree information. The SNP markers did not show clear separation of heterotic groups A and B that were established based on combining ability tests through diallel and line x tester analyses. Our results demonstrated large differences among the SNP markers in terms of reproducibility, ease of scoring, polymorphism, minor allele frequency and polymorphic information content. About 40% of the SNPs in the multiplexed chip-based GoldenGate assays were found to be uninformative in this study and we recommend 644 of the 1065 for low to medium density genotyping in tropical maize germplasm using uniplex assays.

 Conclusions

 There were high genetic distance and low kinship coefficients among most pairs of lines, clearly indicating the uniqueness of the majority of the inbred lines in these maize breeding programs. The results from this study will be useful to breeders in selecting best parental combinations for new breeding crosses, mapping population development and marker assisted breeding.