Boosting predictive ability of tropical maize hybrids via genotype-by-environment interaction under multivariate GBLUP models.

Genomic selection has been implemented in several plant and animal breeding programs and it has proven to improve efficiency and maximize genetic gains. Phenotypic data of grain yield was measured in 147 maize (Zea mays L.) singlecross hybrids at 12 environments. Single-cross hybrids genotypes were inferred based on their parents (inbred lines) via single nucleotide polymorphism (SNP) markers obtained from genotyping-by-sequencing (GBS). Factor analytic multiplicative genomic best linear unbiased prediction (GBLUP) models, in the framework of multienvironment trials, were used to predict grain yield performance of unobserved tropical maize single-cross hybrids. Predictions were performed for two situations: untested hybrids (CV1), and hybrids evaluated in some environments but missing in others (CV2). Models that borrowed information across individuals through genomic relationships and within individuals across environments presented higher predictive accuracy than those models that ignored it. For these models, predictive accuracies were up to 0.4 until eight environments were considered as missing for the validation set, which represents 67% of missing data for a given hybrid. These results highlight the importance of including genotype-by-environment interactions and genomic relationship information for boosting predictions of tropical maize single-cross hybrids for grain yield

A mixed-model QTL analysis for sugarcane multiple-harvest-location trial data

Os programas de melhoramento da cana-de-açúcar demandam aproximadamente 12 anos para a obtenção de um novo cultivar. Assim, os marcadores moleculares podem ser usados como uma ferramenta valiosa, uma vez que possibilitamo estudo da arquitetura genética de caracteres quantitativos, ajudando a reduzir este tempo. Embora a cana-de-açúcar seja uma cultura perene, para a qual o desempenho genotípico é avaliado através de ensaios estabelecidos ao longo de diferentes locais e cortes, a maior parte dos estudos de mapeamento de QTLs ignora a existência de interação entre QTLs, corte e local (QTL × H × L). Neste contexto, o presente trabalho apresenta uma estratégia que foi desenvolvida para a detecção de QTLs em cana-de-açúcar, com base em modelos mistos e mapeamento por intervalo, considerando diferentes estruturas de (co)variância que permitem supor heterogeneidade de variâncias genéticas e existência de correlações genéticas entre cortes e locais. A metodologia de modelos mistos foi aplicada aos dados de uma população segregante obtida a partir do cruzamento entre dois cultivares pré-comerciais de cana-de-açúcar, constituída por 100 indivíduos avaliados em dois locais (Piracicaba e Jaú, SP, Brasil) e em três cortes para produção (toneladas de cana por hectare, TCH), produção de açúcar (toneladas de Pol por hectare, TPH), porcentagem de fibra e Pol (teor de sacarose). A análise fenotípica resultou na seleção do modelo não-estruturado, que assume heterogeneidade de variâncias e existência de correlação genética específica para cada combinação de corte e local, para todos os caracteres avaliados. Na análise de mapeamento, foram detectados 50 QTLs, incluindo 14 QTLs para TCH, 15 para TSH, 10 para Pol e 11 para Fibra. Além disso, os resultados mostram que os efeitos das interações entre QTL e corte (QTL × H), QTL e local (QTL × L) e QTL, corte e local (QTL × H × L) foram importantes para todos os caracteres avaliados. Do total de QTLs identificados, 33 (66 %) apresentaram algum tipo de interação e apenas 17 (34 %) mostraram mesmo efeito entre as diferentes combinações de corte e local. Estes resultados fornecem informações importantes para o entendimento da base genética de caracteres quantitativos relacionados com produção e teor de sacarose em cana-de-açúcar.Sugarcane breeding programs take at least twelve years to develop new commercial cultivars. Thus, molecular markers can be used as a valuable tool since they offer the possibility to study the genetic architecture of quantitative traits, helping to reduce this time. Although the performance of genotypes in sugarcane breeding programs has been evaluated across a range of locations and harvest years, since sugarcane is a perennial crop, many of the QTL detection methods ignore QTL by harvest by location interaction (QTL × H × L). In this work, a strategy for QTL detection in sugarcane was developed, based on mixed models and interval mapping, considering different (co)variance structures for the modeling of heterogeneous genetic variances and genetic correlations between harvests and locations. The mixed model approach was applied to a data set provided by a segregating population developed from a cross between two pre-commercial Brazilian cultivars, consisted of 100 individuals planted in two locations in 2003 (Piracicaba and Jaú, SP, Brazil) and evaluated in the first, second and third subsequent harvest years for cane yield (tonnes of cane per hectare, TCH), sugar yield (tonnes of sugar per hectare, TSH), fiber percent and Pol (sucrose content). Phenotypic analysis provided the selection of the unstructured model, which allows the assumption of heterogeneity of variance and presence of a specific genetic correlation for each combination of harvest and location. In the QTL mapping procedure, 50 QTLs were detected, including 14 QTLs for TCH, 15 for TSH, 10 for Pol and 11 for Fiber. In addition, the results show that QTL by harvest (QTL × H), QTL by location (QTL × L) and QTL by harvest by location (QTL × H × L) interaction effects were important for all evaluated traits. From the total of QTLs identified, 33 (66%) had some interaction and only 17 (34%) showed stable effects across the different combinations of harvest and location. These results can provide useful information to understand the genetic control of complex traits related with sugarcane production and sucrose content

Universal tail sequence-SSR applied to molecular characterization of tropical maize hybrids

The development of efficient and low-cost genotyping methods is essential to precise genetic characterization of cultivars. Here, we present a system based on fluorescently labeled universal tail sequence primers (UTSP) to resolve microsatellite (SSR) markers as an alternative for molecular fingerprinting of maize. A set of 20 SSRs using the UTSP presented an average polymorphic information content of 0.84, which provided a probability of random identity ranging from 10−7 to 10−14, and a minimum exclusion power of 99.99998 % in a group of 48 tropical maize single-cross hybrids traded in Brazil. The genetic diversity analysis based on multidimensional scaling explained approximately 28 % of the total variance for the first two coordinates, tending to group the hybrids according to their respective origin. Additionally, this genotyping system presented a high distinctiveness capacity, which is widely recommended for genetic purity and fingerprinting analyses. Thus, this marker system has a strong potential as a tool for complementary analysis of distinguishability, uniformity and stability required for cultivar registration

Scientia Agricola Universal tail sequence-SSR applied to molecular characterization of tropical maize

ABSTRACT: The development of efficient and low-cost genotyping methods is essential to precise genetic characterization of cultivars. Here, we present a system based on fluorescently labeled universal tail sequence primers (UTSP) to resolve microsatellite (SSR) markers as an alternative for molecular fingerprinting of maize. A set of 20 SSRs using the UTSP presented an average polymorphic information content of 0.84, which provided a probability of random identity ranging from 10 −7 to 10 −14 , and a minimum exclusion power of 99.99998 % in a group of 48 tropical maize single-cross hybrids traded in Brazil. The genetic diversity analysis based on multidimensional scaling explained approximately 28 % of the total variance for the first two coordinates, tending to group the hybrids according to their respective origin. Additionally, this genotyping system presented a high distinctiveness capacity, which is widely recommended for genetic purity and fingerprinting analyses. Thus, this marker system has a strong potential as a tool for complementary analysis of distinguishability, uniformity and stability required for cultivar registration

Universal tail sequence-SSR applied to molecular characterization of tropical maize hybrids

ABSTRACT The development of efficient and low-cost genotyping methods is essential to precise genetic characterization of cultivars. Here, we present a system based on fluorescently labeled universal tail sequence primers (UTSP) to resolve microsatellite (SSR) markers as an alternative for molecular fingerprinting of maize. A set of 20 SSRs using the UTSP presented an average polymorphic information content of 0.84, which provided a probability of random identity ranging from 10−7 to 10−14, and a minimum exclusion power of 99.99998 % in a group of 48 tropical maize single-cross hybrids traded in Brazil. The genetic diversity analysis based on multidimensional scaling explained approximately 28 % of the total variance for the first two coordinates, tending to group the hybrids according to their respective origin. Additionally, this genotyping system presented a high distinctiveness capacity, which is widely recommended for genetic purity and fingerprinting analyses. Thus, this marker system has a strong potential as a tool for complementary analysis of distinguishability, uniformity and stability required for cultivar registration

Hitos tecnológicos que cambiaron el rol de Brasil en la producción de maíz: 30 años de crecimiento para convertirse en importante actor del escenario mundial, una revisión

Corn has experienced a true revolution in Brazil in the last 30 years (agricultural harvests from 1991/92 to 2021/2022). Currently, the country has established itself as the third producer and second exporter worldwide of this cereal, with a production of more than 100 million tons of this grain per agricultural year. In this period, soybean cultivation stands out as the great driver of technological advances, leading corn and other crops to more prominent positions and transforming grain production systems; previously monoculture or rotation, to more intensified systems, with two (or more) agricultural crops per year in the same area. The Brazilian Cerrado region, previously considered unsuitable for agriculture, is today the great barn of grain production in Brazil. In these three decades of escalation in corn production, some legal and technological milestones stand out, such as the Law for the Protection of Cultivars and its regulations (since 1997), the direct sowing system, the cultivation of corn in the second harvest (after soybean), and the use of biotechnologies. These factors were decisive for the growth of maize production to exceed by more than 3.6 times the volume of the 1991/92 agricultural season, while the area devoted to maize cultivation increased only 1.5 times. Increases in productivity are linked to technologies and knowledge applied to the management of production systems, soybean-corn, and not only in an isolated crop; allowing greater advances in the gross production of both grains (recent yields in the corn harvest are about 2.5 times higher than 30 years ago). This article shows data and facts that allowed Brazil to get out of a position of vulnerability, in terms of corn supply, to become an important player in the production and marketing of this cereal worldwide.En los últimos 30 años (cosechas agrícolas de 1991/92 a 2021/2022), el maíz ha vivido una verdadera revolución en Brasil. Actualmente, el país se ha consolidado como el tercer productor y segundo exportador de este cereal, con una producción de más de 100 millones de toneladas de este grano por año agrícola. En este período, el cultivo de soja se destaca como el gran impulsor de los avances tecnológicos, llevando al maíz y a otros cultivos a posiciones más destacadas y transformando los sistemas de producción de granos; que antes eran de monocultivo o rotación, a sistemas más intensificados, con dos (o más) cultivos agrícolas por año en la misma área. La región del Cerrado brasileño, antes considerada no apta para la agricultura, es hoy el gran granero de la producción de granos de Brasil. En estas tres décadas de escalada en la producción de maíz, se destacan algunos hitos legales y tecnológicos, como la Ley de Protección de Cultivares y su reglamento (desde 1997), el Sistema de Siembra Directa, el cultivo de maíz en segunda cosecha o “safrinha” (después de la soja) y el uso de biotecnologías. Estos factores fueron determinantes para que el crecimiento de la producción de maíz superara en más de 3,6 veces el volumen de la campaña agrícola 1991/92, mientras que el área destinada al cultivo de maíz aumentó sólo 1,5 veces. Los incrementos en la productividad están ligados a tecnologías y conocimientos aplicados a la gestión de los sistemas productivos, en el binomio soja-maíz, y no solo en un cultivo aislado; permitiendo mayores avances en la producción bruta de ambos granos (rendimientos recientes en la cosecha de maíz son unas 2,5 veces mayores que hace 30 años). Este trabajo presenta datos y hechos que permitieron a Brasil salir de una posición de vulnerabilidad, en cuanto a la oferta de grano de maíz, para convertirse en un actor importante en la producción y comercialización de este cereal a nivel mundial

Evaluation of the potential of lines and hybrids of biomass sorghum

Mutant genotypes of biomass sorghum for low lignin - bmr (brown midrib) and sensitive to photoperiod are interesting for the production of second-generation ethanol. This research aimed to estimate the combining ability between lines A and R of biomass sorghum, both carrying the bmr-6 allele, for bioenergy potential. Three male-sterile lines (A) and ten fertility restorative lines (R) were used, generating 30 hybrids bmr and sensitive to photoperiod. The 30 hybrids, their parents, and six controls were evaluated in a triple lattice design (7 × 7), in two experimental areas of Embrapa Maize and Sorghum, in Sete Lagoas and Nova Porteirinha (Minas Gerais). These lines were crossed in a partial diallel design, based on the Griffing IV model (1956) adapted for partial diallel by Miranda Filho and Geraldi (1984). The evaluated traits were: days to flowering (DTF, days after sowing), plant height (PH, m), fresh biomass yield (FBY, ton.ha−1), dry matter (DM, %), and dry matter yield (DMY, t. ha−1). In addition, the FAI-BLUP selection Index was used to assist the selection of hybrids that simultaneously meet favorable traits. Results revealed that treatments x environment interaction had a significant effect (p < 0.01) for all traits. Moreover, genetic variability was detected between lines A and R, which can be explored by the pyramiding of their favorable alleles, aiming at developing superior hybrids for the production of second-generation bioethanol

A multi-environment trials diallel analysis provides insights on the inheritance of fumonisin contamination resistance in tropical maize

In maize, the fungi that cause Fusarium ear rot result not only in decreased grain yield and quality, but also grain contamination by fumonisin. This study investigated the inheritance of fumonisin contamination resistance (FCR) in tropical maize, based on a multi-environment trials diallel analysis via mixed models. For this purpose, based on 13 inbred lines, single-cross hybrids were created and assessed in three environments. A mixed model diallel joint analysis across environments was performed, considering the existence of environment-specific variances and correlations between pairs of environments for general combining ability (GCA) and specific combining ability (SCA) effects, and additive genomic relationship between inbred lines for the prediction of GCA and SCA. For all environments, the SCA variance had a higher magnitude than the GCA variance, indicating a predominance of the dominance effects underlying FCR in tropical maize. Moreover, the proportion of the variance among single-cross hybrids that was due to GCA varied from 16 to 22 % across environments, suggesting that SCA is important to predict the hybrids performance. Through modeling variance–covariance structures for GCA and SCA, it was possible to observe that the GCA effects were stable, whereas the SCA effects were specific for each environment. Therefore, these results suggest that the selection of the best parents for the development of new inbred lines can be carried out through the average performance across the evaluated environments. Due to the importance of SCA effects and their complex interaction with environments, the selection of superior hybrids should be performed into specific environments