Genomic Prediction from Multi-Environment Trials of Wheat Breeding.

Genomic prediction relates a set of markers to variability in observed phenotypes of cultivars and allows for the prediction of phenotypes or breeding values of genotypes on unobserved individuals. Most genomic prediction approaches predict breeding values based solely on additive effects. However, the economic value of wheat lines is not only influenced by their additive component but also encompasses a non-additive part (e.g., additive × additive epistasis interaction). In this study, genomic prediction models were implemented in three target populations of environments (TPE) in South Asia. Four models that incorporate genotype × environment interaction (G × E) and genotype × genotype (GG) were tested: Factor Analytic (FA), FA with genomic relationship matrix (FA + G), FA with epistatic relationship matrix (FA + GG), and FA with both genomic and epistatic relationship matrices (FA + G + GG). Results show that the FA + G and FA + G + GG models displayed the best and a similar performance across all tests, leading us to infer that the FA + G model effectively captures certain epistatic effects. The wheat lines tested in sites in different TPE were predicted with different precisions depending on the cross-validation employed. In general, the best prediction accuracy was obtained when some lines were observed in some sites of particular TPEs and the worse genomic prediction was observed when wheat lines were never observed in any site of one TPE.

Genomic Prediction of Resistance to Tan Spot, Spot Blotch and Septoria Nodorum Blotch in Synthetic Hexaploid Wheat.

Genomic prediction combines molecular and phenotypic data in a training population to predict the breeding values of individuals that have only been genotyped. The use of genomic information in breeding programs helps to increase the frequency of favorable alleles in the populations of interest. This study evaluated the performance of BLUP (Best Linear Unbiased Prediction) in predicting resistance to tan spot, spot blotch and Septoria nodorum blotch in synthetic hexaploid wheat. BLUP was implemented in single-trait and multi-trait models with three variations: (1) the pedigree relationship matrix (A-BLUP), (2) the genomic relationship matrix (G-BLUP), and (3) a combination of the two matrices (A+G BLUP). In all three diseases, the A-BLUP model had a lower performance, and the G-BLUP and A+G BLUP were statistically similar (p ≥ 0.05). The prediction accuracy with the single trait was statistically similar (p ≥ 0.05) to the multi-trait accuracy, possibly due to the low correlation of severity between the diseases.

Seed and seedling quality of three chilis (Capsicum annuum L) native to Oaxaca, Mexico / Qualidade de sementes e plântulas de três pimentas (Capsicum annuum L) endêmicas de Oaxaca, México

The diversity of chilis in Oaxaca is one of the most extensive in Mexico. Growers select seeds in the traditional manner; information on its quality is unknown. The aim of this research was to compare the physical and physiological quality of seeds and seedlings of three native types to chili (Huacle, De agua and Pasilla) and of the commercial Green pepper as control. Fifteen variables were evaluated in seed and twelve in seedlings. The laboratory experiments were established under a completely randomized design. Means of the variables were compared using the Tukey test (=0.05). Results showed that Pasilla chili had the highest values in seed size and weight, which was 1.44 g heavier than the control and 2.09 to 3.73 g higher than native types. Haucle chili and green pepper had a 90% germination rate, while chili De agua and Pasilla chili had germination rates of 51 and 38%, respectively. Huacle chili had the highest germination rate index (29.89) and seedling vigor index (992.25). The top highest values of number of normal seedlings were obtained in the control and Huacle chili seedlings (72 and 88%); also, the latter had the longest plumule (3.36 cm) and radicle (7.67 cm) values. Both Huacle and Pasilla chili seedlings had larger values in height, stem thickness, number of leaves, leaf area and slenderness index than De agua and Green pepper. Huacle chili had good physical and physiological quality similar to the seeds of the commercial Green pepper.(AU)

Oaxaca é umas das regiões de maior diversidade de espécies de pimentas do México. Os agricultores selecionam sementes da maneira tradicional; informações sobre sua qualidade são desconhecidas. O objetivo desta pesquisa foi comparar a qualidade física e fisiológica de sementes e mudas de três tipos nativos de pimenta (Huacle, De Agua e Pasilla) e pimenta verde comercial como controle. Quinze variáveis foram avaliadas em sementes e doze em mudas. As experiências de laboratório foram estabelecidas sob um delineamento inteiramente casualizado. As médias das variáveis foram comparadas pelo teste de Tukey (=0.05). Os resultados mostraram que o Pasilla apresentou os maiores valores em tamanho e peso de sementes, 1,44 g mais pesado que o controle e 2,09 a 3,73 g maior que os demais tipos de pimenta nativa. A pimenta Huacle e a pimenta verde tiveram 90% de germinação de 90%, enquanto que De Agua e Pasilla foi de 51 e 38%, respectivamente. A pimienta Huacle apresentou os maiores índices de taxa de germinação (29,89) e de vigor de plântulas (992,25). Os maiores valores máximos no número de mudas normais foram obtidos no controle e na pimenta Huacle (72 e 88%). Além disso, este último apresentou os maiores valores de plúmula (3,36 cm) e radícula (7,67 cm). As mudas do Huacle e Pasilla apresentaram maiores valores em altura, espessura do caule, número de folhas, área foliar e índice de esbelto em relação à pimenta, De agua e ao controle. O Huacle apresentou boa qualidade física e fisiológica, semelhante às sementes da pimentão comercial.(AU)

Seed and seedling quality of three chilis (Capsicum annuum L.) native to Oaxaca, Mexico / Qualidade de sementes e plântulas de três pimentas (Capsicum annuum L.) endêmicas de Oaxaca, México

ABSTRACT: The diversity of chilis in Oaxaca is one of the most extensive in Mexico. Growers select seeds in the traditional manner; information on its quality is unknown. The aim of this research was to compare the physical and physiological quality of seeds and seedlings of three native types to chili (Huacle, De agua and Pasilla) and of the commercial Green pepper as control. Fifteen variables were evaluated in seed and twelve in seedlings. The laboratory experiments were established under a completely randomized design. Means of the variables were compared using the Tukey test (α=0.05). Results showed that Pasilla chili had the highest values in seed size and weight, which was 1.44 g heavier than the control and 2.09 to 3.73 g higher than native types. Haucle chili and green pepper had a 90% germination rate, while chili De agua and Pasilla chili had germination rates of 51 and 38%, respectively. Huacle chili had the highest germination rate index (29.89) and seedling vigor index (992.25). The top highest values of number of normal seedlings were obtained in the control and Huacle chili seedlings (72 and 88%); also, the latter had the longest plumule (3.36 cm) and radicle (7.67 cm) values. Both Huacle and Pasilla chili seedlings had larger values in height, stem thickness, number of leaves, leaf area and slenderness index than De agua and Green pepper. Huacle chili had good physical and physiological quality similar to the seeds of the commercial Green pepper.

RESUMO: Oaxaca é umas das regiões de maior diversidade de espécies de pimentas do México. Os agricultores selecionam sementes da maneira tradicional; informações sobre sua qualidade são desconhecidas. O objetivo desta pesquisa foi comparar a qualidade física e fisiológica de sementes e mudas de três tipos nativos de pimenta (Huacle, De Agua e Pasilla) e pimenta verde comercial como controle. Quinze variáveis foram avaliadas em sementes e doze em mudas. As experiências de laboratório foram estabelecidas sob um delineamento inteiramente casualizado. As médias das variáveis foram comparadas pelo teste de Tukey (α=0.05). Os resultados mostraram que o Pasilla apresentou os maiores valores em tamanho e peso de sementes, 1,44 g mais pesado que o controle e 2,09 a 3,73 g maior que os demais tipos de pimenta nativa. A pimenta Huacle e a pimenta verde tiveram 90% de germinação de 90%, enquanto que De Agua e Pasilla foi de 51 e 38%, respectivamente. A pimienta Huacle apresentou os maiores índices de taxa de germinação (29,89) e de vigor de plântulas (992,25). Os maiores valores máximos no número de mudas normais foram obtidos no controle e na pimenta Huacle (72 e 88%). Além disso, este último apresentou os maiores valores de plúmula (3,36 cm) e radícula (7,67 cm). As mudas do Huacle e Pasilla apresentaram maiores valores em altura, espessura do caule, número de folhas, área foliar e índice de esbelto em relação à pimenta, De agua e ao controle. O Huacle apresentou boa qualidade física e fisiológica, semelhante às sementes da pimentão comercial.

Quantitative trait locus mapping associated with earliness and fruit weight in tomato

The flowering time is regarded as an important factor that affects yield in various crops. In order to understand how the molecular basis controlling main components of earliness in tomato (Solanum lycopersicum L.), and to deduce whether the correlation between fruit weight, days to flowering and seed weight, is caused by pleiotropic effects or genetic linkage, a QTLs analysis was carried out using an F2 interspecific population derived from the cross of S. lycopersicum and S. pimpinellifolium. The analysis revealed that most of the components related to earliness were independent due to the absence of phenotypic correlation and lack of co-localization of their QTLs. QTLs affecting the flowering time showed considerable variation over time in values of explained phenotypic variation and average effects, which suggested dominance becomes more evident over time. The path analysis showed that traits such as days to flowering, seed weight, and length of the first leaf had a significant effect on the expression of fruit weight, confirming that their correlations were due to linkage. This result was also confirmed in two genomic regions located on chromosomes 1 and 4, where despite showing high co-localization of QTLs associated to days to flowering, seed weight and fruit weight, the presence and absence of epistasis in dfft1.1 × dftt4.1 and fw1.1 × fw4.1, suggested that the linkage was the main cause of the co-localization.(AU)

Quantitative trait locus mapping associated with earliness and fruit weight in tomato

The flowering time is regarded as an important factor that affects yield in various crops. In order to understand how the molecular basis controlling main components of earliness in tomato (Solanum lycopersicum L.), and to deduce whether the correlation between fruit weight, days to flowering and seed weight, is caused by pleiotropic effects or genetic linkage, a QTLs analysis was carried out using an F2 interspecific population derived from the cross of S. lycopersicum and S. pimpinellifolium. The analysis revealed that most of the components related to earliness were independent due to the absence of phenotypic correlation and lack of co-localization of their QTLs. QTLs affecting the flowering time showed considerable variation over time in values of explained phenotypic variation and average effects, which suggested dominance becomes more evident over time. The path analysis showed that traits such as days to flowering, seed weight, and length of the first leaf had a significant effect on the expression of fruit weight, confirming that their correlations were due to linkage. This result was also confirmed in two genomic regions located on chromosomes 1 and 4, where despite showing high co-localization of QTLs associated to days to flowering, seed weight and fruit weight, the presence and absence of epistasis in dfft1.1 × dftt4.1 and fw1.1 × fw4.1, suggested that the linkage was the main cause of the co-localization.