Posts Tagged ‘crop science’

Optimal design of preliminary yield trials with genome-wide markers

Posted by Carelia Juarez on , in Journal Articles

Published in Crop Science, 2013

Jeffrey B. Endelman, Gary N. Atlin, Yoseph Beyene, Kassa Semagn, Xuecai Zhang, Mark E. Sorrells and Jean-Luc Jannink

Previous research on genomic selection (GS) has focused on predicting unphenotyped lines. GS can also improve the accuracy of phenotyped lines at low heritability, e.g., in a preliminary yield trial (PYT). Our first objective was to estimate this effect within a biparental family, using multi-location yield data for barley and maize. We found that accuracy increased with training population size and was higher with an unbalanced design spread across multiple locations than when testing all entries in one location. The latter phenomenon illustrates that when seed is limited, genome-wide markers enable broader sampling from the target population of environments. Our second objective was to explore the optimum allocation of resources at a fixed budget. When PYT selections are advanced for further testing, we propose a new metric for optimizing genetic gain: Rax, the expected maximum genotypic value of the selections. The optimal design did not involve genotyping more progeny than were phenotyped, even when the cost of creating and genotyping each line was only 0.25 the cost of one yield plot unit (YPU). At a genotyping cost of 0.25 YPU, GS offered up to a 5% increase in genetic gain compared to phenotypic selection for a budget of 200 YPU per family. To increase genetic gains further, the  training population must be expanded beyond the full-sib family under selection, using close relatives of the parents as a source of prediction accuracy.

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.

New articles from CIMMYT: Identification of drought, heat, and combined drought and heat tolerant donors in maize

Posted by Carelia Juarez on , in Journal Articles

Published in Crop Science 53 (4) : 1335-1346, 2013

Jill E. Cairns, Jose Crossa, P. H. Zaidi, Pichet Grudloyma, Ciro Sanchez, Jose Luis Araus, Suriphat Thaita, Dan Makumbi, Cosmos Magorokosho, Marianne Bänziger, Abebe Menkir, Sarah Hearne and Gary N. Atlin

Low maize (Zea maysL.) yields and the impacts of climate change on maize production highlight the need to improve yields in eastern and southern Africa. Climate projections suggest higher temperatures within drought-prone areas. Research in model species suggests that tolerance to combined drought and heat stress is genetically distinct from tolerance to either stress alone, but this has not been confirmed in maize. In this study we evaluated 300 maize inbred lines testcrossed to CML539. Experiments were conducted under optimal conditions, reproductive stage drought stress, heat stress, and combined drought and heat stress. Lines with high levels of tolerance to drought and combined drought and heat stress were identified. Significant genotype × trial interaction and very large plot residuals were observed; consequently, the repeatability of individual managed stress trials was low. Tolerance to combined drought and heat stress in maize was genetically distinct from tolerance to individual stresses, and tolerance to either stress alone did not confer tolerance to combined drought and heat stress. This finding has major implications for maize drought breeding. Many current drought donors and key inbreds used in widely grown African hybrids were susceptible to drought stress at elevated temperatures. Several donors tolerant to drought and combined drought and heat stress, notably La Posta Sequia C7-F64-2-6-2-2 and DTPYC9-F46-1-2-1-2, need to be incorporated into maize breeding pipelines.

Comparison of the performance of best linear unbiased estimation and best linear unbiased prediction of genotype effects from zoned Indian maize data

Posted by Carelia Juarez on , in Journal Articles

Published in Crop Science, 2013

K. Kleinknecht, J. Möhring, K.P. Singh, P.H. Zaidi, G.N. Atlin and H.P. Piepho

The maize (Zea mays L.) growing area in India is divided into five zones for cultivar testing. During triannual testing of genotypes in official trials within the All-India Coordinated Maize Improvement Program (AICMIP), a large number of entries is rejected each year. Therefore, only a low number of entries is carried forward to the advanced stage of testing. The subdivision of the breeding sites into zones results in limited data per zone. Hence, the question arises how to select the best genotypes per zone and how information can be borrowed across zones to improve the accuracy of selection within zones. We compared the performance of best linear unbiased prediction (BLUP) using the correlation of genetic effects between zones with best linear unbiased estimation (BLUE) based on data per zone. In both cases, data were analyzed using a mixed model. We used simulations to calculate correlations between the true simulated values and the predicted genotype values obtained by BLUE and BLUP using the same models. The data structure and the variance components used in simulations were based on the analysis of 40 triannual series of four different maize maturity groups. Best linear unbiased prediction outperformed BLUE in 38 out of 40 series and on average across all series. An advantage of BLUP was observed for varying genetic correlations between zones. We conclude that the use of BLUP enhanced the estimation accuracy in zoned AICMIP maize testing trials and can be recommended for future use in these trials.


Physical Mapping of Puroindoline b-2 Genes in Wheat using ‘Chinese Spring’ Chromosome Group 7 Deletion Lines

Posted by Carelia Juarez on , in Journal Articles

Published in Crop Science 52 (6) : 2674-2678, 2012

Hongwei Geng, Brian S. Beecher, He Zhonghu  and Craig F. Morris

The puroindoline genes (Puroindoline a-D1 and Puroindoline b-D1), located very near to the distal end of the short arm of chromosome 5D (distal to fraction arm length of 0.78) have a significant effect on grain hardness. Puroindoline b-2 (Pinb-2) is another puroindoline gene family that exists as a homoeologous series on group 7 chromosomes. However, a more detailed localization (physical mapping) of the Pinb-2 genes has not been conducted. In the present study, 24 group 7 long-arm chromosome deletion stocks of ‘Chinese Spring’ were used to physically map three Pinb-2 variant genes: Pinb-2v1, Pinb-2v2, and Pinb-2v4. All three genes were found to be physically located on the most distal 0.11 to 0.16 fraction arm length of chromosomes 7AL, 7BL, and 7DL in Chinese Spring. These results contribute insight into wheat (Triticum aestivum L.) genome synteny, structure, and organization and provide a useful metric for germplasm and population relationships. Future studies may further resolve the physical mapping of Pinb-2 genes at the ends of group 7 chromosomes and contribute to a better understanding of the molecular and genetic basis of kernel hardness.

Strategies to subdivide a target population of environments: Results from the CIMMYT-led maize hybrid testing programs in Africa

Posted by Carelia Juarez on , in Journal Articles

Published in Crop Science 52 (5) : 2143-2152, 2012

Vanessa S. Windhausen, Silke Wagener, Cosmos Magorokosho, Dan Makumbi, Bindiganavile Vivek, Hans-Peter Piepho, Albrecht E. Melchinger and Gary N. Atlin

To develop stable and high-yielding maize (Zea mays L.) hybrids for a diverse target population of environments (TPE), breeders have to decide whether greater gains result from selection across the undivided TPE or within more homogeneous subregions. Currently, CIMMYT subdivides the TPE in eastern and southern Africa into climatic and geographic subregions. To study the extent of specific adaptation to these subregions and to determine whether selection within subregions results in greater gains than selection across the undivided TPE, yield data of 448 maize hybrids evaluated in 513 trials across 17 countries from 2001 to 2009 were used. The trials were grouped according to five subdivision systems into climate, altitude, geographic, country, and yield-level subregions. For the first four subdivision systems, genotype × subregion interaction was low, suggesting broad adaptation of maize hybrids across eastern and southern Africa. In contrast, genotype × yield-level interactions and moderate genotypic correlations between low- and high-yielding subregions were observed. Therefore, hybrid means should be estimated by stratifying the TPE considering the yield-level effect as fixed and appropriately weighting information from both subregions. This strategy was at least 10% better in terms of predicted gains than direct selection using only data from the low- or high-yielding subregion and should facilitate the identification of hybrids that perform well in both subregions.

Genomic prediction of breeding values when modeling genotype × environment interaction using pedigree and dense molecular markers

Posted by Carelia Juarez on , in Journal Articles

Published in Crop Science 52 (2) : 707-719, 2012

Juan Burgueño, Gustavo de los Campos, Kent Weigel and José Crossa

Genomic selection (GS) has become an important aid in plant and animal breeding. Multienvironment (multitrait) models allow borrowing of information across environments (traits), which could enhance prediction accuracy. This study presents multienvironment (multitrait) models for GS and compares the predictive accuracy of these models with: (i) multienvironment analysis without pedigree and marker information, and (ii) multienvironment pedigree or/and marker-based models. A statistical framework for incorporating pedigree and molecular marker information in models for multienvironment data is described and applied to data that originate from wheat (Triticum aestivum L.) multienvironment trials. Two prediction problems relevant to plant breeders are considered: (CV1) predicting the performance of untested genotypes (“newly” developed lines), and (CV2) predicting the performance of genotypes that have been evaluated in some environments but not in others. Results confirmed the superiority of models using both marker and pedigree information over those based on pedigree information only. Models with pedigree and/or markers had better predictive accuracy than simple linear mixed models that do not include either of these two sources of information. We concluded that the evaluation of such trials can benefit greatly from using multienvironment GS models.



Development of functional markers for a Lipoxygenase gene TaLox-B1 on chromosome 4BS in common wheat

Posted by Carelia Juarez on , in Journal Articles

Published in Crop Science 52 (2): 568-576, 2012

Hongwei Geng, Xianchun Xia, Liping Zhang, Yanying Qu and Zhonghu He

Lipoxygenase (LOX) activity in grain influences the color and processing quality of wheat (Triticum spp.)-based products. Characterization of LOX genes and development of functional markers are of importance for marker-assisted selection in common wheat (Triticum aestivum L.) breeding. In the present study, the full-length genomic DNA (gDNA) sequence of a LOX gene (designated TaLox-B1) located on chromosome 4BS was characterized by in silico cloning and experimental validation. Two complementary dominant sequence tagged site (STS) markers, LOX16 and LOX18, were developed based on the single nucleotide polymorphism (SNP) of two alleles at the TaLox-B1 locus, amplifying 489- and 791-bp fragments in cultivars with higher and lower LOX activities, respectively. The two markers were mapped on chromosome 4BS using a doubled haploid (DH) population derived from Zhongyou 9507 × CA9632, a set of Chinese Spring nullisomic–tetrasomic lines, ditelosomic line 4BS, and Langdon (LDN) 4D(4B) chromosome substitution line. Quantitative trait loci (QTL) analysis indicated that TaLox-B1 co-segregated with the two functional markers and was closely linked to simple sequence repeat (SSR) locus Xgwm251 on chromosome 4BS with a genetic distance of 1.8 cM. LOX16 and LOX18 were validated on 198 Chinese wheat cultivars and advanced lines and showed highly significant (p < 0.01) associations with LOX activity. These results suggested that LOX16 and LOX18, co-segregating with TaLox-B1, could be used for the improvement of color attributes of noodles and other wheat-based products in wheat breeding programs.



Genetic yield gains of the CIMMYT international semi-arid wheat yield trials from 1994 to 2010

Posted by Carelia Juarez on , in Journal Articles

Published in Crop Science  52 (4): 1543-1552, 2012

Y. Manès , H. F. Gomez, L. Puhl, M. Reynolds, H. J. Braun and R. Trethowan

Genetic progress for yield has been assessed globally in the semi-arid wheat yield trials (SAWYTs) of the International Maize and Wheat Improvement Center (CIMMYT) over a 17-yr period. Grain yield expressed as a percentage of the long-term check cultivar Dharwar Dry has increased at approximately 1% yr−1 between 1994 and 2010. In real terms, yield has been increased at a rate of 31 kg ha−1 yr−1. The rate of yield increase in high-yielding environments was twice that of low-yielding environments. The average yield of low-yielding sites are significantly correlated with the average yield of high-yielding sites (p < 0.001), and many of the highest-yielding lines of the various SAWYT performed well at both low- and high-yielding sites. The key parents Attila and Pastor were consistently high yielding in several of the early SAWYT. In later trials their derivatives were also high yielding. The line Vorobey, developed by crossing Pastor with a synthetic derivative, showed outstanding yield in SAWYT 11 and 12. The performance of CIMMYT lines compared to local check cultivars was relatively stable over time. A success rate was calculated as the ratio of the number of sites where a given line is superior to the local check divided by the total number of sites. On average, the success rate of the 10% best lines was 61% in low-yielding sites and 62% in high-yielding sites.

Genetic gains for grain yield in CIMMYT spring bread wheat across international environments

Posted by Carelia Juarez on , in Journal Articles

Published in Crop Science 52 (4): 1522-1533, 2012

R. C. Sharma, J. Crossa, G. Velu, J. Huerta-Espino, M. Vargas, T. S. Payne and R. P. Singh

The Global Wheat Program of the International Maize and Wheat Improvement Center (CIMMYT) develops and distributes improved germplasm targeted toward various wheat growing regions of developing world. The objective of our study was to quantify the genetic yield gains in CIMMYT’s spring bread wheat (Triticum aestivum L.) in the Elite Spring Wheat Yield Trial (ESWYT) distributed over the past 15 yr (1995–2009) as determined by the performance of entries across 919 environments in 69 countries. To determine the annual genetic gains, differences in mean yields of the five highest yielding entries from mean trial yield and mean yield of the widely grown international check ‘Attila’ were regressed over 15 yr of ESWYT testing. Across locations in all countries, mean yields of the five highest yielding entries showed an annual gain of 27.8 kg ha−1 (0.65%) compared to Attila. Annual yield gains in mega-environment 1 (ME1) (optimally irrigated), ME2 (high rainfall), Egypt, India, and Pakistan were 27.4 (0.55%), 21.4 (0.62%), 111.6 (1.13%), 32.5 (0.83%), and 18.5 kg ha−1 (0.5%), respectively. These results demonstrate continuous genetic yield gains in the elite spring bread wheat lines developed and distributed by CIMMYT and the positive outcomes achieved through breeding and the international exchange of elite spring wheat germplasm that have benefited national programs throughout the world.