A singular value decomposition Bayesian multiple-trait and multiple-environment genomic model.

Today, breeders perform genomic-assisted breeding to improve more than one trait. However, frequently there are several traits under study at one time, and the implementation of current genomic multiple-trait and multiple-environment models is challenging. Consequently, we propose a four-stage analysis for multiple-trait data in this paper. In the first stage, we perform singular value decomposition (SVD) on the resulting matrix of trait responses; in the second stage, we perform multiple trait analysis on transformed responses. In stages three and four, we collect and transform the traits back to their original state and obtain the parameter estimates and the predictions on these scale variables prior to transformation. The results of the proposed method are compared, in terms of parameter estimation and prediction accuracy, with the results of the Bayesian multiple-trait and multiple-environment model (BMTME) previously described in the literature. We found that the proposed method based on SVD produced similar results, in terms of parameter estimation and prediction accuracy, to those obtained with the BMTME model. Moreover, the proposed multiple-trait method is atractive because it can be implemented using current single-trait genomic prediction software, which yields a more efficient algorithm in terms of computation.

Genetic Gains for Grain Yield in CIMMYT's Semi-Arid Wheat Yield Trials Grown in Suboptimal Environments.

Wheat (Triticum aestivum L.) is a major staple food crop grown worldwide on >220 million ha. Climate change is regarded to have severe effect on wheat yields, and unpredictable drought stress is one of the most important factors. Breeding can significantly contribute to the mitigation of climate change effects on production by developing drought-tolerant wheat germplasm. The objective of our study was to determine the annual genetic gain for grain yield (GY) of the internationally distributed Semi-Arid Wheat Yield Trials, grown during 2002-2003 to 2013-2014 and developed by the Bread Wheat Breeding program at the CIMMYT. We analyzed data from 740 locations across 66 countries, which were classified in low-yielding (LYE) and medium-yielding (MYE) environments according to a cluster analysis. The rate of GY increase (GYC) was estimated relative to four drought-tolerant wheat lines used as constant checks. Our results estimate that the rate of GYC in LYE was 1.8% (38.13 kg ha-1 yr-1), whereas in MYE, it was 1.41% (57.71 kg ha-1 yr-1). The increase in GYC across environments was 1.6% (48.06 kg ha-1 yr-1). The pedigrees of the highest yielding lines through the coefficient of parentage analysis indicated the utilization of three primary sources-'Pastor', 'Baviacora 92', and synthetic hexaploid derivatives-to develop drought-tolerant, high and stably performing wheat lines. We conclude that CIMMYT's wheat breeding program continues to deliver adapted germplasm for suboptimal conditions of diverse wheat growing regions worldwide.

Grain yield, adaptation and progress in breeding for early-maturing and heat-tolerant wheat lines in South Asia.

Maintaining wheat productivity under the increasing temperatures in South Asia is a challenge. We focused on developing early maturing wheat lines as an adaptive mechanism in regions suffering from terminal heat stress and those areas that require wheat adapted to shorter cycles under continual high temperature stress. We evaluated the grain yield performance of early-maturing heat-tolerant germplasm developed by CIMMYT, Mexico at diverse locations in South Asia from 2009 to 2014 and estimated the breeding progress for high-yielding and early-maturing heat-tolerant germplasm in South Asia. Each year the trial comprised of 28 new entries, one CIMMYT check (Baj) and a local check variety. Locations were classified by mega environment (ME); ME1 being the temperate irrigated locations with terminal high temperature stress, and ME5 as hot, sub-tropical, irrigated locations. Grain yield (GY), days to heading (DTH) and plant height (PH) were recorded at each location. Effect of temperature on GY was observed in both ME1 and ME5. Across years, mean minimum temperatures in ME1 and mean maximum temperatures in ME5 during grain filling had significant negative association with GY. The ME1 locations were cooler that those in ME5 in the 5 years of evaluations and had a 1-2 t/ha higher GY. A mean reduction of 20 days for DTH and 20 cm in PH was observed in ME5. Negative genetic correlations of -0.43 to -0.79 were observed between GY and DTH in South Asia during 2009-2014. Each year, we identified early-maturing germplasm with higher grain yield than the local checks. A positive trend was observed while estimating the breeding progress across five years for high-yielding early-maturing heat tolerant wheat compared to the local checks in South Asia. The results suggests the potential of the high-yielding early-maturing wheat lines developed at CIMMYT in improving wheat production and maintaining genetic gains in South Asia.

Effect of Lesion Age, Humidity, and Fungicide Application on Sporulation of Alternaria alternata, the Cause of Brown Spot of Tangerine.

Alternaria brown spot, caused by Alternaria alternata, causes yield losses and fruit blemishes on many tangerines and their hybrids in most citrus areas of the world where susceptible cultivars are grown. Although the conditions affecting infection and disease severity are known, little information is available on inoculum production on infected tissue. We found that sporulation on leaves began about 10 days after symptoms developed, was abundant from 20 to 40 days, and declined thereafter. Conidial production was far greater on leaf than on fruit or twig lesions. Spore production per unit area of leaf lesion was greater on the more susceptible hybrids, Minneola and Orlando tangelos, than on the less susceptible Murcott tangor. At 74% relative humidity, conidial production on leaf lesions was low, but it was abundant at 85, 92.5, 96, and 100%. Application of QoI or copper fungicides, but not ferbam, suppressed sporulation on leaf lesions for about 14 to 21 days after application. Additional applications did not appear to be more effective than a single spray in reducing inoculum production.