Genomic selection (GS) is a promising strategy for enhancing genetic gain. We investigated the accuracy of genomic estimated breeding values (GEBV) in four inter-related synthetic populations that ...underwent several cycles of recurrent selection in an upland rice-breeding program. A total of 343 S2:4 lines extracted from those populations were phenotyped for flowering time, plant height, grain yield and panicle weight, and genotyped with an average density of one marker per 44.8 kb. The relative effect of the linkage disequilibrium (LD) and minor allele frequency (MAF) thresholds for selecting markers, the relative size of the training population (TP) and of the validation population (VP), the selected trait and the genomic prediction models (frequentist and Bayesian) on the accuracy of GEBVs was investigated in 540 cross validation experiments with 100 replicates. The effect of kinship between the training and validation populations was tested in an additional set of 840 cross validation experiments with a single genomic prediction model. LD was high (average r2 = 0.59 at 25 kb) and decreased slowly, distribution of allele frequencies at individual loci was markedly skewed toward unbalanced frequencies (MAF average value 15.2% and median 9.6%), and differentiation between the four synthetic populations was low (FST ≤0.06). The accuracy of GEBV across all cross validation experiments ranged from 0.12 to 0.54 with an average of 0.30. Significant differences in accuracy were observed among the different levels of each factor investigated. Phenotypic traits had the biggest effect, and the size of the incidence matrix had the smallest. Significant first degree interaction was observed for GEBV accuracy between traits and all the other factors studied, and between prediction models and LD, MAF and composition of the TP. The potential of GS to accelerate genetic gain and breeding options to increase the accuracy of predictions are discussed.
Current advances in sequencing technologies and bioinformatics revealed the genomic background of rice, a staple food for the poor people, and provided the basis to develop large genomic variation ...databases for thousands of cultivars. Proper analysis of this massive resource is expected to give novel insights into the structure, function, and evolution of the rice genome, and to aid the development of rice varieties through marker assisted selection or genomic selection. In this work we present sequencing and bioinformatics analyses of 104 rice varieties belonging to the major subspecies of Oryza sativa. We identified repetitive elements and recurrent copy number variation covering about 200 Mbp of the rice genome. Genotyping of over 18 million polymorphic locations within O. sativa allowed us to reconstruct the individual haplotype patterns shaping the genomic background of elite varieties used by farmers throughout the Americas. Based on a reconstruction of the alleles for the gene GBSSI, we could identify novel genetic markers for selection of varieties with high amylose content. We expect that both the analysis methods and the genomic information described here would be of great use for the rice research community and for other groups carrying on similar sequencing efforts in other crops.
The apomictic reproductive mode of Brachiaria (syn. Urochloa) forage species allows breeders to faithfully propagate heterozygous genotypes through seed over multiple generations. In Brachiaria, ...reproductive mode segregates as single dominant locus, the apospory-specific genomic region (ASGR). The AGSR has been mapped to an area of reduced recombination on Brachiaria decumbens chromosome 5. A primer pair designed within ASGR-BABY BOOM-like (BBML), the candidate gene for the parthenogenesis component of apomixis in Pennisetum squamulatum, was diagnostic for reproductive mode in the closely related species B. ruziziensis, B. brizantha, and B. decumbens. In this study, we used a mapping population of the distantly related commercial species B. humidicola to map the ASGR and test for conservation of ASGR-BBML sequences across Brachiaria species.
Dense genetic maps were constructed for the maternal and paternal genomes of a hexaploid (2n = 6x = 36) B. humidicola F
mapping population (n = 102) using genotyping-by-sequencing, simple sequence repeat, amplified fragment length polymorphism, and transcriptome derived single nucleotide polymorphism markers. Comparative genomics with Setaria italica provided confirmation for x = 6 as the base chromosome number of B. humidicola. High resolution molecular karyotyping indicated that the six homologous chromosomes of the sexual female parent paired at random, whereas preferential pairing of subgenomes was observed in the apomictic male parent. Furthermore, evidence for compensated aneuploidy was found in the apomictic parent, with only five homologous linkage groups identified for chromosome 5 and seven homologous linkage groups of chromosome 6. The ASGR mapped to B. humidicola chromosome 1, a region syntenic with chromosomes 1 and 7 of S. italica. The ASGR-BBML specific PCR product cosegregated with the ASGR in the F
mapping population, despite its location on a different carrier chromosome than B. decumbens.
The first dense molecular maps of B. humidicola provide strong support for cytogenetic evidence indicating a base chromosome number of six in this species. Furthermore, these results show conservation of the ASGR across the Paniceae in different chromosomal backgrounds and support postulation of the ASGR-BBML as candidate genes for the parthenogenesis component of apomixis.
Beans of the species
L., also known as cacao, are the raw material to produce chocolate. Colombian cacao has been classified as a fine flavor cacao that represents the 5% of cacao world's production. ...Colombian genetic resources from this species are conserved in
and in-field germplasm banks, since
has recalcitrant seeds to desication and long-term storage. Currently, the collection of
of the Colombian Corporation of Agricultural Research (CORPOICA) has approximately 700 germplasm accessions. We conducted a molecular analysis of Corpoica's cacao collection and a morphological characterization of some accessions with the goal to study its genetic diversity and population structure and, to select interesting accessions for the cacao's breeding program. Phenotypic evaluation was performed based on 18 morphological traits and 4 biochemical traits. PCA analysis of morphological traits explained 60.6% of the total variation in seven components and 100% of the total variation of biochemical traits in four components, grouping the collection in 4 clusters for both variables. We explored 565 accessions from Corpoica's germplasm and 252 accessions from reference populations using 96 single nucleotide polymorphism (SNP) molecular markers. Molecular patterns of cacao Corpoica's collection were obtained amplifying specific alleles in a Fluidigm platform that used integrated circuits of fluids. Corpoica's collection showed highest genetic diversity Expected Heterozygosity (
= 0.314), Observed Heterozygosity (
= 0.353) that is reduced when reference populations were included in the dataset (
= 0.294,
= 0.261). The collection was divided into four clusters based on population structure analysis. Cacao accessions from distinct groups showed some taxonomic concordance and reflected their geographic origins. For instance, accessions classified as Criollo were clearly differentiated in one group and we identified two new Colombian genetic groups. Using a number of allelic variations based on 87 SNP markers and 22 different morphological/biochemical traits, a core collection with a total of 232 accessions was selected as a primary genetic resource for cacao breeders.
Genomic selection is a worthy breeding method to improve genetic gain in recurrent selection breeding schemes. The integration of multi-generation and multi-location information could significantly ...improve genomic prediction models in the context of shuttle breeding. The Cirad-CIAT upland rice breeding program applies recurrent genomic selection and seeks to optimize the scheme to increase genetic gain while reducing phenotyping efforts. We used a synthetic population (PCT27) of which S
0
plants were all genotyped and advanced by selfing and bulk seed harvest to the S
0:2
, S
0:3
, and S
0:4
generations. The PCT27 was then divided into two sets. The S
0:2
and S
0:3
progenies for PCT27A and the S
0:4
progenies for PCT27B were phenotyped in two locations: Santa Rosa the target selection location, within the upland rice growing area, and Palmira, the surrogate location, far from the upland rice growing area but easier for experimentation. While the calibration used either one of the two sets phenotyped in one or two locations, the validation population was only the PCT27B phenotyped in Santa Rosa. Five scenarios of genomic prediction and 24 models were performed and compared. Training the prediction model with the PCT27B phenotyped in Santa Rosa resulted in predictive abilities ranging from 0.19 for grain zinc concentration to 0.30 for grain yield. Expanding the training set with the inclusion of the PCT27A resulted in greater predictive abilities for all traits but grain yield, with increases from 5% for plant height to 61% for grain zinc concentration. Models with the PCT27B phenotyped in two locations resulted in higher prediction accuracy when the models assumed no genotype-by-environment (G × E) interaction for flowering (0.38) and grain zinc concentration (0.27). For plant height, the model assuming a single G × E variance provided higher accuracy (0.28). The gain in predictive ability for grain yield was the greatest (0.25) when environment-specific variance deviation effect for G × E was considered. While the best scenario was specific to each trait, the results indicated that the gain in predictive ability provided by the multi-location and multi-generation calibration was low. Yet, this approach could lead to increased selection intensity, acceleration of the breeding cycle, and a sizable economic advantage for the program.
Abstract
Population breeding through recurrent selection is based on the repetition of evaluation and recombination among best-selected individuals. In this type of breeding strategy, early ...evaluation of selection candidates combined with genomic prediction could substantially shorten the breeding cycle length, thus increasing the rate of genetic gain. The objective of this study was to optimize early genomic prediction in an upland rice (Oryza sativa L.) synthetic population improved through recurrent selection via shuttle breeding in two sites. To this end, we used genomic prediction on 334 S0 genotypes evaluated with early generation progeny testing (S0:2 and S0:3) across two sites. Four traits were measured (plant height, days to flowering, grain yield, and grain zinc concentration) and the predictive ability was assessed for the target site. For days to flowering and plant height, which correlate well among sites (0.51–0.62), an increase of up to 0.4 in predictive ability was observed when the model was trained using the two sites. For grain zinc concentration, adding the phenotype of the predicted lines in the nontarget site to the model improved the predictive ability (0.51 with two-site and 0.31 with single-site model), whereas for grain yield the gain was less (0.42 with two-site and 0.35 with single-site calibration). Through these results, we found a good opportunity to optimize the genomic recurrent selection scheme and maximize the use of resources by performing early progeny testing in two sites for traits with best expression and/or relevance in each specific environment.
Formación del profesorado en Latinoamérica Quintero, María Constanza Cano; Ordoñez, Edward Javier
Revista de ciencias sociales (Maracaibo, Venezuela),
04/2021, Volume:
27, Issue:
2
Journal Article
Peer reviewed
Open access
La formación del profesorado en la actualidad reviste de gran interés para académicos, investigadores y organizaciones mundiales que velan por la educación de los pueblos; dado que se reconoce en la ...cualificación de este gremio, uno de los aspectos que determinan la calidad educativa y el consecuente avance de la sociedad. En este estudio se pretende identificar y describir las tendencias de las investigaciones y escritos académicos sobre la Formación de los docentes en Latinoamerica. Se presenta un estudio cualitativo, descriptivo de tipo documental. Los resultados evidencian que la educación del profesorado ha sido tema de la mayoria de reformas educativas en los paises de este continente, las cuales fueron motivadas, no solo por ajustes económicos y políticos, acontecieron también como producto de las luchas de los colectivos docentes. Se concluye, que hay particularidades de tipo cultural en la manera como se forman los maestros en América Látina, pero existen aspectos comunes como, la influencia de modelos económicos globales en las tendencias actuales de la formación del profesorado o como la necesidad de enfoques educativos que propendan por el desarrollo de competencias investigativas en los docentes y que fortalezcan el saber pedagógico más allá de modelos meramente didácticos o metodológicos.
With the aim to find new sources of resistance to rice hoja blanca (white leaf) disease, transmitted by the insect Tagosodes orizicolus, 660 genotypes were evaluated under greenhouse and field ...conditions. Seven resistant genotypes were identified, and genomic studies were performed to demonstrate that the resistance in these sources is genetically different from that of Fedearroz 2000, which is currently the variety with the most resistance to hoja blanca. These new resistance sources constitute a resource that can be used to sustainably extend hoja blanca disease management throughout all of the rice-growing regions of tropical America. This is the first report of hoja blanca resistance in indica rice and different from that of Fedearroz 2000.
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