Posts Tagged ‘Plant Breeding’

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.

 

Doubled haploid technology in maize breeding: theory and practice

Posted by Jose Juan Caballero on , in CIMMYT Publications

Prasanna, B.M.;  Vijay Chaikam and George Mahuku

Abstract: This manual is primarily intended for maize breeders in the national agricultural research systems (NARS) and small and medium enterprise (SME) seed companies in the developing countries  who would like to better underst and utilizes the doubled haploid (DH) technology in breeding programs. It is a compilation and consolidation of knowledge accumulated through scientific contributions of several maize geneticists and breeders worldwide as well as protocols successfully developed (in collaboration with University of Hohenheim, Germany) and being used by the CIMMYT Global Maize Program in DH line development, especially in Mexico. An overview of the utility and applications of DH technology in maize breeding is presented first in the Manual, followed by Chapters on in vivo maternal haploid induction using haploid inducers, haploid kernel detection using anthocyanin markers, chromosome doubling of haploids, deriving DH seed from colchicine‐treated plants, DH in commercial maize breeding, integrating molecular markers in DH‐based breeding pipeline, and finally, access to tropicalized haploid inducers and DH service from CIMMYT.

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.

Recombination frequency variation in maize as revealed by genomewide single-nucleotide polymorphisms

Posted by on , in Journal Articles

Published in Plant Breeding 130(5): 533-539, 2011

Recombination frequency variation in maize as revealed by genomewide single-nucleotide polymorphisms

Mohammad Farkhari, Yanli Lu, Trushar Shah, Shihuang Zhang, Mohammad R. Naghavi, Tingzhao Rong and  Yunbi Xu

Recombination frequency greatly affects selection efficiency in plant breeding. A high-density single-nucleotide polymorphism (SNP) map integrated with physical map and other molecular maps is very useful for characterizing genetic recombination variation. In this study, recombination frequency in maize was investigated through SNP linkage maps constructed with three recombinant inbred line populations. The integrated map consisted of 1443 molecular markers, including 1155 SNPs, spanning 1346 cM. A 100-fold difference in recombination frequency was observed between different chromosomal regions, ranging from an average of 0.09 cM/Mb for pericentromeric regions to 7.08 cM/Mb for telomeric regions. Recombination suppression in non-centromeric regions identified nine recombination-suppressed regions, one of which likely contained condensed heterochromatin (knobs). Recombination variation along chromosomes was highly predictable for pericentromeric and telomeric regions, but population-specific with 4.5-fold difference for the same marker interval across the three populations or specific chromosome regions because of the presence of knobs. As recombination variation can be identified and well characterized as shown in this study, the related information will facilitate future genetic studies, gene cloning and marker-assisted plant breeding.

Participatory Varietal Selection of Wheat for Micro-Niches of Kathmandu Valley

Posted by on , in Journal Articles

Published in Journal of Sustainable Agriculture 33: 745-756

Participatory Varietal Selection of Wheat for Micro-Niches of Kathmandu Valley 

D. B. Thapa;  A. Mudwari;  R. K. Basnet;  S. Sharma;  G. Ortiz-Ferrara;  B. Sharma; K. Murphy

The diversity of agro-environmental conditions among wheat-based farming systems in the mountainous regions of Nepal may favor the development and production of multiple narrowly adapted varieties over a few broadly adapted varieties. Sixteen genotypes were tested using Participatory Varietal Selection (PVS) trials at farmers’ fields in three districts in the Kathmandu Valley. Grain yield was the trait most preferred by farmers, followed by tillering, resistance to diseases, drought, and lodging. Farmer selection of optimal genotypes varied over time and location depending on agronomic and climatic pressures, indicating a preference by farmers for growing multiple, narrowly adapted varieties. Production potential of PVS genotypes averaged up to 142% greater than the most widely grown variety, RR21. With farmer participation in the selection process in different agro-ecological micro-niches of Nepal, both yield potential and yield stability of wheat should increase significantly, thereby providing farmers with the economic means to sustain the current small-scale agriculture suited to the mountainous terrain.

Genetic variation and environmental stability of grain mineral nutrient concentrations in Triticum dicoccoides under five environments

Posted by on , in Journal Articles

Published in Euphytica 171: 39-52

Genetic variation and environmental stability of grain mineral nutrient concentrations in Triticum dicoccoides under five environments

Hugo Ferney Gomez-Becerra, Atilla Yazici, Levent Ozturk, Hikmet Budak, Zvi Peleg, Alexey Morgounov, Tzion Fahima, Yehoshua Saranga and Ismail Cakmak

 Nineteen wild emmer wheat [Triticum turgidum ssp. dicoccoides (Körn.) Thell.] genotypes were evaluated for the grain concentrations of phosphorous (P), potassium (K), sulfur (S), magnesium (Mg), calcium (Ca), zinc (Zn), manganese (Mn), iron (Fe) and cooper (Cu) under five different environments in Turkey and Israel. Each mineral nutrient has been investigated for the (1) genotype by environment (G × E) interactions, (2) genotype stability, (3) correlation among minerals and (4) mineral stability. Among the macronutrients analyzed, grain concentrations of Ca (range 338–2,034 mg kg−1) and S (range 0.18–0.43%) showed the largest variation. In the case of micronutrients, the largest variation was observed in the grain Mn concentration (range 13–87 mg kg−1). Grain concentrations of Fe and Zn also showed important variation (range 27–86 and 39–115 mg kg−1, respectively). Accessions with higher nutrient concentrations (especially Zn and Fe) had also greater grain weight, suggesting that higher grain Zn and Fe concentrations are not necessarily related to small grain size or weight. Analysis of variance showed that environment was the most important source of variation for K, S, Ca, Fe, Mn and Zn, explaining between 44 and 78% of the total variation and G × E explained between 20 and 40% of the total variation in all the minerals, except for S and Zn where its effect accounted for less than 16%. Genotype was the most important source of variation for Cu (explaining 38% of the total variation). However, genotype effect was also important for Mg, Mn, Zn and S. Sulfur and Zn showed the largest heritability values (77 and 72%, respectively). Iron exhibited low heritability and high ratio value between the G × E and genotype variance components $$ left( {sigma_{text{GE}}^{2} /sigma_{G}^{2} } right) $$, suggesting that specific adaptation for this mineral could be positively exploited. The wild emmer germplasm tested in the current study revealed some outstanding accessions (such as MM 5/4 and 24-39) in terms of grain Zn and Fe concentrations and environmental stability that can be used as potential donors to enhance grain micronutrient concentrations in wheats.

A high-throughput, low cost gel-based SNP assay for positional cloning and marker assisted breeding of useful genes in cereals

Posted by on , in Journal Articles

Published in Plant Breeding 128(4):325-331

A high-throughput, low cost gel-based SNP assay for positional cloning and marker assisted breeding of useful genes in cereals

X. Xu, R. Babu, T. Fujimura and S. Kawasaki

Several SNP (single nucleotide polymorphism) genotyping methods have been developed in the past most of which require sophisticated instrumentation and large initial investments. We describe here a high-throughput SSCP (single strand conformation polymorphism) system on our HEGS (high efficiency genome scanning) platform, which is simple, accurate, cost effective and requires neither restriction digestion of the amplification products nor elaborate post-PCR processing detection. Several parameters critical to SSCP analysis were optimized viz., gel matrix and concentration, gel running temperature, buffer composition, running conditions and PCR primer design so as to identify SNPs in amplicons ranging from 100 to 750 bp in size. A simple post-PCR processing system was developed using fluorescent dye for quick and easy detection of SNP polymorphism. HEGS-SSCP was also found to be useful in uncovering simple sequence repeat differences between different genotypes that differ by one or few di/tri nucleotide repeats. The practical utility of this system is illustrated with two successful efforts towards construction of high resolution linkage maps of a lesion mimic locus on chromosome 7 and a major quantitative trait locus conditioning field blast resistance on chromosome 4 in rice.