Novel strategies for genomic prediction of untested single-cross maize hybrids using unbalanced historical data.

KEY MESSAGE: Weighted outperformed unweighted genomic prediction using an unbalanced dataset representative of a commercial breeding program. Moreover, the use of the two cycles preceding predictions as training set achieved optimal prediction ability. Predicting the performance of untested single-cross hybrids through genomic prediction (GP) is highly desirable to increase genetic gain. Here, we evaluate the predictive ability (PA) of novel genomic strategies to predict single-cross maize hybrids using an unbalanced historical dataset of a tropical breeding program. Field data comprised 949 single-cross hybrids evaluated from 2006 to 2013, representing eight breeding cycles. Hybrid genotypes were inferred based on their parents' genotypes (inbred lines) using single-nucleotide polymorphism markers obtained via genotyping-by-sequencing. GP analyses were fitted using genomic best linear unbiased prediction via a stage-wise approach, considering two distinct cross-validation schemes. Results highlight the importance of taking into account the uncertainty regarding the adjusted means at each step of a stage-wise analysis, due to the highly unbalanced data structure and the expected heterogeneity of variances across years and locations of a commercial breeding program. Further, an increase in the size of the training set was not always advantageous even in the same breeding program. The use of the two cycles preceding predictions achieved optimal PA of untested single-cross hybrids in a forward prediction scenario, which could be used to replace the first step of field screening. Finally, in addition to the practical and theoretical results applied to maize hybrid breeding programs, the stage-wise analysis performed in this study may be applied to any crop historical unbalanced data.

Characteristics of 1555 childhood-onset lupus in three groups based on distinct time intervals to disease diagnosis: a Brazilian multicenter study.

Objective The objective of this study was to compare demographic data, clinical/laboratorial features and disease activity at diagnosis in three different groups with distinct time intervals between onset of signs/symptoms and disease diagnosis. Methods A multicenter study was performed in 1555 childhood-onset systemic lupus erythematosus (American College of Rheumatology criteria) patients from 27 pediatric rheumatology services. Patients were divided into three childhood-onset systemic lupus erythematosus groups: A: short time interval to diagnosis (<1 month); B: intermediate time interval (≥1 and <3 months); and C: long time interval (≥3 months). An investigator meeting was held to define the protocol. Demographic data, SLICC classification criteria and SLEDAI-2 K were evaluated. Results The number of patients in each group was: A = 60 (4%); B = 522 (33.5%); and C = 973 (62.5%). The median age at diagnosis (11.1 (4.2-17) vs. 12 (1.9-17.7) vs. 12.5 (3-18) years, P = 0.025) was significantly lower in group A compared with groups B and C. The median number of diagnostic criteria according to SLICC (7 (4-12) vs. 6 (4-13) vs. 6 (4-12), P < 0.0001) and SLEDAI-2 K (18 (6-57) vs. 16 (2-63) vs. 13 (1-49), P < 0.0001) were significantly higher in group A than the other two groups. The frequency of oral ulcers in the palate (25% vs. 15% vs. 11%, P = 0.003), pleuritis (25% vs. 24% vs. 14%, P < 0.0001), nephritis (52% vs. 47% vs. 40%, P = 0.009), neuropsychiatric manifestations (22% vs. 13% vs. 10%, P = 0.008), thrombocytopenia (32% vs. 18% vs. 19%, P = 0.037), leucopenia/lymphopenia (65% vs. 46% vs. 40%, P < 0.0001) and anti-dsDNA antibodies (79% vs. 66% vs. 61%, P = 0.01) were significantly higher in group A compared with the other groups. In contrast, group C had a less severe disease characterized by higher frequencies of synovitis (61% vs. 66% vs. 71%, P = 0.032) and lower frequencies of serositis (37% vs. 33% vs. 25%, P = 0.002), proteinuria >500 mg/day (48% vs. 45% vs. 36%, P = 0.002) and low complement levels (81% vs. 81% vs. 71%, P < 0.0001) compared with groups A or B. Conclusions Our large Brazilian multicenter study demonstrated that for most childhood-onset systemic lupus erythematosus patients, diagnosis is delayed probably due to mild disease onset. Conversely, the minority has a very short time interval to diagnosis and a presentation with a more severe and active multisystemic condition.

Maize hybrid stability in environments under water restriction using mixed models and factor analysis.

In several crops, the water deficit is perhaps the main limiting factor in the search for high yields. The objective of this study was to evaluate the phenotypic stability of maize hybrids in environments with and without water restriction using the analytical factor (AF) approach. We evaluated 171 maize hybrids in 14 environments, divided into environments with (A1, A2, A3, A4, A5, A6, and A7) and without (A8, A9, A10, A11, A12, A13, and A14) water restriction, over a period of 7 years. Each year, 36 hybrids were evaluated. A square lattice design (6 x 6) was used, with common treatments between years. The characteristics of grain yield (GY), male flowering (MF) and female flowering (FF), plant height (PH), and ear height (EH) were evaluated. Phenotypic adaptability and stability of the hybrids were also verified. Hybrids G66, G99, G86, and G26 were the most stable and showed potential for use in environments with and without water restriction. The AF models showed to be useful for evaluating hybrids over many years, allowing selection of better hybrids with adaptability, specific and general stability, and correlation of hybrids with their production components, in addition to allowing identification of mega-environments that permit stability in the response of the adapted hybrids.

Intraspecific variability of popcorn S7 lines for phosphorus efficiency in the soil.

The expansion of agriculture, coupled with the need for sustainable cropping, is one of the greatest challenges of the scientific community working on the generation of new cultivars adapted to abiotic stress conditions. The aim of this study was to evaluate the variability of popcorn lines as to responsiveness and efficiency in phosphorus use, as a first step towards the implementation of a breeding program interested in the practice of sustainable agriculture. Twenty-five popcorn lines were evaluated in two locations with different phosphorus levels in the soil, using a randomized block design. The following traits were measured: plant height, ear height, female flowering date, male flowering date, male-female flowering interval, ear diameter, ear length, 100-grain weight, grain yield, popping expansion, and expanded popcorn volume per hectare. A combined analysis of variance and test of means were performed, and the lines were classified as to their phosphorus use efficiency, according to their production performance in the different environments. The genetic diversity between the lines was estimated by Tocher's and UPGMA clustering methods, using generalized Mahalanobis distance. Lines L59, P7, P2, P3, P4, P8, P10, P9, L66, L70, L69, and P5 were efficient and responsive, whereas lines L75, L80, L61, L77, L63, L65, P1, L54, L53, L88, and L71 were inefficient and nonresponsive. Genetic variability was greater in the environments with low phosphorus in the soil, suggesting that the selection pressure exerted in the stressing environment is a decisive factor to obtain a higher expression of variability.

Selection of sorghum hybrids grown under aluminum saturation.

The purpose of this study was to evaluate 165 hybrids derived from lines previously selected for aluminum (Al) tolerance. Nine check cultivars were used, eight commercial hybrids and one experimental hybrid. Hybrids were evaluated at three levels of Al saturation (0, 20 and 40% on average). The differences between the environments were significant. Environment with 0% Al saturation yielded 29.5% more than that with 40% Al saturation, showing the importance of genotype selection for acid soils. The best check cultivar was the hybrid DKB550. The hybrids AG1020 and AG1040 also performed well, where the latter was more tolerant but the former more responsive to environment improvement. The hybrid BRS304 was susceptible to high levels of Al saturation. The three commercial BRS hybrids (BRS310, BRS330 and BRS332) performed better than BRS304 at high Al saturation. The hybrid BRS330 was the best BRS hybrid to grow on a field with high Al saturation. The hybrid DKB559 performed well at high Al saturation but did not respond to environment improvement. The hybrids 727029, 727039, 729041, 729095, 729109, AG1040, and DKB550 were tolerant to higher levels of Al saturation and responsive to environment improvement, and showed good stability and adaptability at both low and high Al saturation.