Posts Tagged ‘genetics’

Bacterial colonization of a fumigated alkaline saline soil

Posted by Carelia Juarez on , in Journal Articles

Published in Extremophiles 18 (4) : 733-743, 2014

Bello-Lopez, J.M.; Dominguez-Mendoza, C.A.; Leon-Lorenzana, A.S. de; Delgado-Balbuena, L.; Navarro-Noya, Y.E.; Gomez-Acata, S.; Rodriguez-Valentin, A.; Ruiz-Valdiviezo, V.M.; Luna-Guido, M.;Verhulst, N.; Govaerts, G.; Dendooven, L.

After chloroform fumigating an arable soil, the relative abundance of phylotypes belonging to only two phyla (Actinobacteria and Firmicutes) and two orders [Actinomycetales and Bacillales (mostlyBacillus)] increased in a subsequent aerobic incubation, while it decreased for a wide range of bacterial groups. It remained to be seen if similar bacterial groups were affected when an extreme alkaline saline soil was fumigated. Soil with electrolytic conductivity between 139 and 157 dS m−1, and pH 10.0 and 10.3 was fumigated and the bacterial community structure determined after 0, 1, 5 and 10 days by analysis of the 16S rRNA gene, while an unfumigated soil served as control. The relative abundance of the Firmicutes increased in the fumigated soil (52.8 %) compared to the unfumigated soil (34.2 %), while that of the Bacteroidetes decreased from 16.2 % in the unfumigated soil to 8.8 % in the fumigated soil. Fumigation increased the relative abundance of the genusBacillus from 14.7 % in the unfumigated soil to 25.7 %. It was found that phylotypes belonging to theFirmicutes, mostly of the genus Bacillus, were dominant in colonizing the fumigated alkaline saline as found in the arable soil, while the relative abundance of a wide range of bacterial groups decreased.

Progress towards genetics and breeding for minor genes based resistance to Ug99 and other rusts in CIMMYT high yielding spring wheat

Posted by Carelia Juarez on , in Journal Articles

Published in Journal of Integrative Agriculture 13 (2) : 255-261, 2014

Singh, R.P.; Herrera-Foessel, S.; Huerta-Espino, J.; Sukhwinder Singh; Bhavani, S.; Caixia Lan;Basnet, B.R.

Wheat rusts continue to cause significant losses worldwide despite major efforts given to their genetic control. This is due to frequent evolution and selection of virulence in pathogen overcoming the deployed race-specific resistance genes. Although the life of effective race-specific resistance genes can be prolonged by using gene combinations, an alternative approach being implemented at CIMMYT is to deploy varieties that posses adult plant resistance (APR) based on combinations of minor, slow rusting genes. When present alone, the APR genes do not confer adequate resistance especially under high disease pressure; however, combinations of 4 or 5 minor genes usually result in “near-immunity” or a high level of resistance. Although only a few APR genes are catalogued, various APR QTL are now known and could lead to further characterization of additional genes. Four characterized genes have pleiotropic effects in conferring partial APR to all three rusts and powdery mildew, thus simplifying the task of breeding wheat varieties that are resistant to multiple diseases. Significant progress was made recently in developing high-yielding wheat germplasm that possesses high levels of APR to all three rusts by implementing a Mexico-Kenya shuttle breeding scheme. Parents with APR to Ug99 were hybridized with high yielding parents that had adequate to high levels of APR to leaf rust and yellow rust. Segregating populations and advanced lines from these crosses were selected under high rust pressures in Mexico (leaf rust and yellow rust) and Kenya (Ug99 stem rust and yellow rust) to identify high yielding progenies that possess high to adequate APR to all three rusts. International distribution of these high yielding wheats is underway through CIMMYT international yield trials and screening nurseries. It is expected that several wheat varieties with APR to three rusts will be released and grown in various countries in the near-future that will allow determining the durability of resistance.

QTL for yield and associated traits in the Seri/Babax population grown across several environments in Mexico, in the West Asia, North Africa, and South Asia regions

Posted by Carelia Juarez on , in Journal Articles

Published in Theoretical and Applied Genetics 126 (4) : 971-984, 2013

Marta S. Lopes, Matthew P. Reynolds, C. Lynne McIntyre, Ky L. Mathews, M. R. Jalal Kamali, Moussa Mossad, Yousef Feltaous, Izzat S. A. Tahir, Ravish Chatrath, Francis Ogbonnaya and  Michael Baum

Heat and drought adaptive quantitative trait loci (QTL) in a spring bread wheat population resulting from the Seri/Babax cross designed to minimize confounding agronomic traits have been identified previously in trials conducted in Mexico. The same population was grown across a wide range of environments where heat and drought stress are naturally experienced including environments in Mexico, West Asia, North Africa (WANA), and South Asia regions. A molecular genetic linkage map including 475 marker loci associated to 29 linkage groups was used for QTL analysis of yield, days to heading (DH) and to maturity (DM), grain number (GM2), thousand kernel weight (TKW), plant height (PH), canopy temperature at the vegetative and grain filling stages (CTvg and CTgf), and early ground cover. A QTL for yield on chromosome 4A was confirmed across several environments, in subsets of lines with uniform allelic expression of a major phenology QTL, but not independently from PH. With terminal stress, TKW QTL was linked or pleiotropic to DH and DM. The link between phenology and TKW suggested that early maturity would favor the post—anthesis grain growth periods resulting in increased grain size and yields under terminal stress. GM2 and TKW were partially associated with markers at different positions suggesting different genetic regulation and room for improvement of both traits. Prediction accuracy of yield was improved by 5 % when using marker scores of component traits (GM2 and DH) together with yield in multiple regression. This procedure may provide accumulation of more favorable alleles during selection.

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.

QTL analysis of the spring wheat ‘Chapio’ identifies stable stripe rust resistance despite inter-continental genotype × environment interactions

Posted by Carelia Juarez on , in Journal Articles

Published in Theoretical and Applied Genetics, 2013

E.-N. Yang, G. M. Rosewarne, S. A. Herrera-Foessel,  J. Huerta-Espino,  Z.-X. Tang, C.-F. Sun,  Z.-L. Ren and R. P. Singh

Chapio is a spring wheat developed by CIMMYT in Mexico by a breeding program that focused on multigenic resistances to leaf rust and stripe rust. A population consisting of 277 recombinant inbred lines (RILs) was developed by crossing Chapio with Avocet. The RILs were genotyped with DArT markers (137 randomly selected RILs) and bulked segregant analysis conducted to supplement the map with informative SSR markers. The final map consisted of 264 markers. Phenotyping against stripe rust was conducted for three seasons in Toluca, Mexico and at three sites over two seasons (total of four environments) in Sichuan Province, China. Significant loci across the two inter-continental regions included Lr34/Yr18 on 7DS, Sr2/Yr30 on 3BS, and a QTL on 3D. There were significant genotype × environment interactions with resistance gene Yr31 on 2BS being effective in most of the Toluca environments; however, a late incursion of a virulent pathotype in 2009 rendered this gene ineffective. This locus also had no effect in China. Conversely, a 5BL locus was only effective in the Chinese environments. There were also complex additive interactions. In the Mexican environments, Yr31 suppressed the additive effect of Yr30 and the 3D locus, but not of Lr34/Yr18, while in China, the 3D and 5BL loci were generally not additive with each other, but were additive when combined with other loci. These results indicate the importance of maintaining diverse, multi-genic resistances as Chapio had stable inter-continental resistance despite the fact that there were QTLs that were not effective in either one or the other region.

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.

Maize HapMap2 identifies extant variation from a genome in flux

Posted by Carelia Juarez on , in Journal Articles

Published in Nature Genetics 44 (7) : 803-807, 2012

Jer-Ming Chia, Chi Song, Peter J Bradbury, Denise Costich, Natalia de Leon, John Doebley, Robert J Elshire, Brandon Gaut, Laura Geller, Jeffrey C Glaubitz, Michael Gore, Kate E Guill, Jim Holland, Matthew B Hufford, Jinsheng Lai, Meng Li, Xin Liu, Yanli Lu, Richard McCombie, Rebecca Nelson, Jesse Poland, Boddupalli M Prasanna, Tanja Pyhäjärvi, Tingzhao Rong, Rajandeep S Sekhon, Qi Sun, Maud I Tenaillon, Feng Tian, Jun Wang, Xun Xu, Zhiwu Zhang, Shawn M Kaeppler, Jeffrey Ross-Ibarra, Michael D McMullen, Edward S Buckler, Gengyun Zhang, Yunbi Xu and Doreen Ware

Whereas breeders have exploited diversity in maize for yield improvements, there has been limited progress in using beneficial alleles in undomesticated varieties. Characterizing standing variation in this complex genome has been challenging, with only a small fraction of it described to date. Using a population genetics scoring model, we identified 55 million SNPs in 103 lines across pre-domestication and domesticated Zea mays varieties, including a representative from the sister genus Tripsacum. We find that structural variations are pervasive in the Z. mays genome and are enriched at loci associated with important traits. By investigating the drivers of genome size variation, we find that the larger Tripsacum genome can be explained by transposable element abundance rather than an allopolyploid origin. In contrast, intraspecies genome size variation seems to be controlled by chromosomal knob content. There is tremendous overlap in key gene content in maize and Tripsacum, suggesting that adaptations from Tripsacum (for example, perennialism and frost and drought tolerance) can likely be integrated into maize.



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.

New book in the library : The genome generation

Posted by Carelia Juarez on , in New Acquisitions

The genome generation

Elizabeth Finkel
ISBN: 978-0522856477
Melbourne University Press
xiv, 274 pages

The year 2001 marked the moment when scientists first read the 3 billion letters of DNA that make up the human genome. This breakthrough begged questions such as What have we learned about evolution? How has it changed the way we practice medicine, grow crops, and breed livestock? and Is the genomic revolution an overhyped flop? Answering these and many other queries, this account covers revolutionary genetic developments in areas as diverse as medicine, agriculture, and evolution. From Botswana to Boston and from Australia to Mexico, the contributors to this work reveal what it means to be part of the genome generation.