Posts Tagged ‘Molecular Breeding’

Physical mapping of puroindoline b-2 genes and molecular characterization of a novel variant in durum wheat (Triticum turgidum L.)

Posted by Carelia Juarez on , in Journal Articles

Published in Molecular Breeding  28 (2) : 153-161, 2012

F. Chen, H.-X. Xu, F.-Y. Zhang, X.-C. Xia, Z.-H. He, D.-W. Wang, Z.-D. Dong, K.-H. Zhan, X.-Y. Cheng and D.-Q. Cui

The puroindoline genes (Pina and Pinb) are the functional components of the common or bread wheat (Triticum aestivum L.) grain hardness locus that are responsible for kernel texture. In this study, four puroindoline b2 variants were physically mapped using nulli-tetrosomic lines of bread wheat cultivar Chinese Spring and substitution lines of durum wheat (Triticum turgidum L.) cultivar Langdon. Results indicated that Pinb2v1 was on 7D of Chinese Spring, Pinb2v2 on 7B of Chinese Spring, Pinb2v3 on 7B of Chinese Spring and Langdon, and Pinb2v4 on 7A of Chinese Spring and Langdon. A new puroindoline b2 variant, designated Pinb2v5, was identified at the puroindoline b2 locus of durum wheat cultivar Langdon, with a difference of only five single nucelotide polymorphisms compared with Pinb2v4. Sequencing results indicated that, in comparison with the Pinb2v3 sequence (AM99733 and GQ496618 with one base-pair modification of G to T at 6th position, designated Pinb2v3a) in bread wheat cultivar Witchta, the coding region of Pinb2v3 in 12 durum wheat cultivars had a single nucleotide change from T to C at the 311th position, resulting in a corresponding amino acid change from valine to alanine at the 104th position. This new allele was designated Pinb2v3b. The study of puroindoline b2 gene polymorphism in CIMMYT and Italian durum wheat germplasm and discovery of a novel puroindoline b2 variant could provide useful information for further understanding the molecular and genetic basis of kernel hardness and illustrating gene duplication events in wheat.

Microsatellite mapping identifies TTKST-effective stem rust resistance gene in wheat cultivars VL404 and Janz

Posted by Carelia Juarez on , in Journal Articles

Published in Molecular Breeding, 2012

Urmil K. Bansal, Rebecca Zwart, Sridhar Bhavani, Ruth Wanyera, Vidya Gupta and Harbans S. Bariana

Wheat cultivar VL404 carries seedling resistance to Puccinia graminis f. sp. tritici pathotype TTKST. Monogenic segregation for seedling resistance was observed in a VL404/WL711 recombinant inbred line population and the resistance locus was temporarily designated SrVL. Bulked segregant analysis using Diversity Arrays Technology markers located SrVL on chromosome 2BL. Detailed simple sequence repeat mapping placed SrVL between gwm120 and wmc175, both at genetic distances of 3.3 cM. Based on adult plant responses of Janz and VL404 in India and Kenya, we expected these  cultivars to carry the same gene against TTKST. A subset of Diamondbird/Janz doubled haploid (DH) population showed monogenic       segregation, when tested against TTKST and the locus was temporarily named SrJNZ. SrVL-linked markers gwm120 and wmc175 flanked SrJNZ at a similar genetic distance, thereby confirming our hypothesis. Chromosome 2BL carries Sr9, Sr16 and Sr28. Sr9 is a multi-allelic locus and all known alleles of Sr9 and Sr16 are ineffective against TTKSK and its derivatives. A recombination value of 16.7 cM between Sr9g-linked stripe rust resistance gene Yr7 and SrJNZ in Diamondbird/Janz DH population suggested that SrJNZ is not an allele at the Sr9 locus. Based on comparison of published genetic distances between Lr13, Sr9, Sr28 and Sr16 with that observed in this study, we concluded SrVL and SrJNZ to be Sr28. This gene was contributed by a common parent Gabo, which also exhibited resistance against TTKST. Sr28-linked markers gwm120 and wmc175 confirmed the presence of this gene in a high proportion of Australian cultivars that showed stem rust resistance in Kenya.  These markers can be used for marker-assisted pyramiding of Sr28 with other stem rust resistance genes.

 

Genetic gain and cost efficiency of marker-assisted selection of maize for improved resistance to multiple foliar pathogens

Posted by Carelia Juarez on , in Journal Articles

Published in  Molecular Breeding 29(2): 515-527, 2012

Godfrey Asea, Bindiganavile S. Vivek, Patrick E. Lipps and Richard C. Pratt

Northern corn leaf blight (NCLB) caused by Exserohilum turcicum, gray leaf spot (GLS) caused by Cercospora zeaemaydis and maize streak caused by maize streak Mastrevirus (MSV) are the most destructive foliar diseases limiting maize production in sub-Saharan Africa. Most foliar diseases of maize are managed using quantitative (partial) resistance, and previous studies have reported quantitative trait loci associated with host resistance (rQTL). Our objective was to compare the genetic gain and costs resulting from phenotypic, genotypic, and marker-assisted selection of partially inbred lines derived from many families for resistance to infection by three foliar pathogens. We developed a population of 410 F2:3 families by crossing inbred line CML202 with a breeding line designated VP31. These families were planted in nurseries inoculated separately with each pathogen. We conducted one cycle of early generation pedigree selection using three different procedures, phenotypic, genotypic, and marker/phenotypic index, for improvement of resistance to each pathogen. We used simple sequence repeat (SSR) markers flanking six target rQTL associated with partial resistance. Broad- and narrow-sense heritability estimates were also obtained for the F2:3 families, and selected and non-selected F2:4 families. Genetic gains resulting from the selection procedures were determined. Gene action of the candidate rQTL was determined using orthogonal contrasts. Estimates of costs based on lower boundary values indicated that the cost of marker-based selection was lower than that of phenotypic selection. Our results indicate that molecular markers linked to target rQTL can facilitate pyramiding resistance to multiple diseases during early generation pedigree selection.

Characterization of a cell wall invertase gene TaCwi-A1 on common wheat chromosome 2A and development of functional markers

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Published in Molecular Breeding 29(1): 43-52, 2012

Dongyun Ma, Jun Yan, Zhonghu He, Ling Wu and Xianchun Xia

Cell wall invertase (CWI) is a critical enzyme for sink tissue development and carbon partition, and has a high association with kernel weight. Characterization of Cwi genes and development of functional markers are of importance for marker-assisted selection in wheat breeding. In the present study, the full-length genomic DNA sequence of a Cwi gene located on wheat chromosome 2A, designated TaCwiA1, was characterized by in silico cloning and experimental validation. TaCwiA1 comprises seven exons and six introns, with 3,676 bp in total, and an open reading frame (ORF) of 1,767 bp. A pair of complementary dominant markers, CWI21 and CWI22, was developed based on allelic variations at the TaCwiA1 locus. A 404-bp PCR fragment was amplified by CWI21 in varieties with lower kernel weights, whereas a 402-bp fragment was generated by CWI22 in the varieties with higher kernel weights. The markers CWI21 and CWI22 were located on chromosome 2AL using a F2:3 population from a cross Doumai/Shi 4185, and a set of Chinese Spring nullisomic–tetrasomic lines. They were linked to the SSR locus Xbarc152AL with a genetic distance of 10.9 cM. QTL analysis indicated that TaCwiA1 could explain 4.8% of phenotypic variance for kernel weight over 2 years. Two sets of Chinese landraces and two sets of commercial wheat varieties were used to validate the association of CWI21 and CWI22 with kernel weight. The results indicated that the functional markers CWI21 and CWI22 were closely related to kernel weight and could be used in wheat breeding for improving grain yield.

Genetic structures of the CIMMYT international yield trial targeted to irrigated environments

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Published in Molecular Breeding 29(2): 529-541, 2012

Susanne Dreisigacker, Hailemichael Shewayrga, Jose Crossa, Vivi N. Arief, Ian H. DeLacy, Ravi P. Singh, Mark J. Dieters and Hans-Joachim Braun

International yield trials are assembled by CIMMYT to disseminate promising wheat breeding materials worldwide. To assess the genomic structure and linkage disequilibrium (LD) within this germplasm, wheat lines disseminated during 25 years of the Elite Spring Wheat Yield Trial (ESWYT) targeted for irrigated environments of the world were genotyped with the high-throughput Diversity Arrays Technology (DArT) marker system. Analyses of population structure assigned the ESWYT germplasm into five major sub-populations that are shaped by prominent CIMMYT wheat lines and their descendants. Based on genetic distance, we concluded that a constant level of genetic diversity was maintained over the years of ESWYT dissemination. Genetic distance between the individual ESWYT lines significantly increased when the ESWYT were grouped according to the differences in years of ESWYT dissemination, suggesting a systematic change in allele frequencies over time, most probably due to breeding and directional selection. By means of multiple regression analyses, 78 markers displaying a significant change in allele frequency across years were identified and interpreted as an indicator for constant selection. The markers identified were partly associated with grain yield, leaf, stem, and yellow rust and point to key genomic regions for further investigation. Large numbers of adjacent DArT marker pairs showed significant LD across the ESWYT population and within each of the five sub-populations identified. Sub-population differentiation measured by the fixation index and average genetic distance were highly correlated with LD levels, suggesting that the sub-populations themselves explain much of the LD.