Insights and protocols for discrimination of sugarcane clones by dissimilarity measures on RGB and NIR data.

In sugarcane breeding, dense experiments have been considered in the initial phase (T1), such as the Simplified System (SS) of genotype selection. In this method, the seedlings of each family are transplanted directly from the seed box to the field, forming a kind of carpet. Despite the practical aspect of the method, selection problems are common, as stalks from the same individual within the family are subject to being taken to later evaluation stages, to the detriment of stalks from different individuals. To facilitate the discrimination of stalks of the same family in SS, we evaluated using RGB images (red:green:blue) and NIR (near infrared) spectra. We applied Euclidean distance (D) and Mahalanobis distance (D2) dissimilarity measures to the image and spectral data to distinguish stalks with different genotypes. RGB and NIR data were taken from type +1 leaf samples collected from two experimental blocks, totaling 31 evaluated families. The analyzes were carried out in two stages. In the first stage, we sought to evaluate the classification capacity using RGB images and NIR spectra, using D as a measure of dissimilarity. In the second step, we developed and validated a protocol using RGB images to classify clones, with D2 as a dissimilarity measure. Preliminary results, with distance D, allowed to discriminate clones based on the distance of the evaluated attributes and their combinations. In addition, with the analyzes using the D distance, it was identified that only the use of the R attribute (red band) would give satisfactory results for the second stage, which was the proposed analysis protocol, applying the D2 distance. The D2 statistic and associated p-value confirmed the protocol's usefulness in discriminating stalks in SS, especially stalks from the same families.

Linkage disequilibrium and haplotype block patterns in popcorn populations.

Linkage disequilibrium (LD) analysis provides information on the evolutionary aspects of populations. Recently, haplotype blocks have been used to increase the power of quantitative trait loci detection in genome-wide association studies and the prediction accuracy of genomic selection. Our objectives were as follows: to compare the degree of LD, LD decay, and LD decay extent in popcorn populations; to characterize the number and length of haplotype blocks in the populations; and to determine whether maize chromosomes also have a pattern of interspaced regions of high and low rates of recombination. We used a biparental population, a synthetic, and a breeding population, genotyped for approximately 75,000 single nucleotide polymorphisms (SNPs). The sample size ranged from 190 to 192 plants. For the whole-genome LD and haplotype block analyses, we assumed a window of 500 kb. To characterize the block and step patterns of LD in the populations, we constructed LD maps by chromosome, defining a cold spot as a chromosome segment including SNPs with the same LDU position. The LD and haplotype block analyses were also performed at the intragenic level, selecting 12 genes related to zein, starch, cellulose, and fatty acid biosynthesis. The populations with the higher and lower frequencies of |D'| values greater than 0.75 were the biparental (65-74%) and the breeding population (26-58%), respectively. There were slight differences between the populations regarding the average distance for SNPs with |D'| values greater than 0.75 (in the range of approximately 207 to 229 kb). The level of LD expressed by the r2 values was low in the populations (0.02, 0.04, and 0.04, on average) but comparable to some non-isolated human populations. The frequency of r2 values greater than 0.75 was lower in the biparental population (0.2-0.5%) and higher in the other populations (0.2-1.6%). The average distance for SNPs with r2 values greater than 0.75 was much higher in the biparental population (approximately 80 to 126 kb). In the other populations, the ranges were approximately 6 to 19 and 6 to 35 kb. The heatmaps for the regions covered by the first 100 SNPs in each chromosome, in each population (1 to 3.3 Mb, approximately), provided evidence that the comparatively few high r2 values (close to 1.0) occurred only for SNPs in close proximity, especially in the synthetic and breeding populations. Due to the reduced number of SNPs in the haplotype blocks (2 to 3) in the populations, it is not expected advantage of a haplotype-based association study as well as genomic selection along generations. The results concerning LD decay (rapid decay after 5-10 kb) and LD decay extent (along up to 300 kb) are in the range observed with maize inbred line panels. The LD maps indicate that maize chromosomes had a pattern of regions of extensive LD interspaced with regions of low LD. However, our simulated LD map provides evidence that this pattern can reflect regions with differences in allele frequencies and LD levels (expressed by |D'|) and not regions with high and low rates of recombination.

Relevance of genetic relationship in GWAS and genomic prediction.

The objective of this study was to analyze the relevance of relationship information on the identification of low heritability quantitative trait loci (QTLs) from a genome-wide association study (GWAS) and on the genomic prediction of complex traits in human, animal and cross-pollinating populations. The simulation-based data sets included 50 samples of 1000 individuals of seven populations derived from a common population with linkage disequilibrium. The populations had non-inbred and inbred progeny structure (50 to 200) with varying number of members (5 to 20). The individuals were genotyped for 10,000 single nucleotide polymorphisms (SNPs) and phenotyped for a quantitative trait controlled by 10 QTLs and 90 minor genes showing dominance. The SNP density was 0.1 cM and the narrow sense heritability was 25%. The QTL heritabilities ranged from 1.1 to 2.9%. We applied mixed model approaches for both GWAS and genomic prediction using pedigree-based and genomic relationship matrices. For GWAS, the observed false discovery rate was kept below the significance level of 5%, the power of detection for the low heritability QTLs ranged from 14 to 50%, and the average bias between significant SNPs and a QTL ranged from less than 0.01 to 0.23 cM. The QTL detection power was consistently higher using genomic relationship matrix. Regardless of population and training set size, genomic prediction provided higher prediction accuracy of complex trait when compared to pedigree-based prediction. The accuracy of genomic prediction when there is relatedness between individuals in the training set and the reference population is much higher than the value for unrelated individuals.

Intervalos entre podas de duas variedades de mandioca / Intervals between prunings of two cassava varieties

Este experimento foi conduzido com o objetivo de avaliar o efeito do intervalo entre podas em duas variedades de mandioca. O ensaio foi instalado na área experimental da Universidade Estadual do Sudoeste da Bahia, Campus de Vitória da Conquista, no período de dezembro de 2008 a julho de 2010, utilizando-se o delineamento em blocos ao acaso, com dez tratamentos e três repetições. Os tratamentos foram arranjados segundo esquema fatorial 2x5, formados pela combinação entre duas variedades de mandioca (Caitité e Sergipe) e cinco intervalos entre podas (dois, quatro, seis e oito meses após o plantio e testemunha - sem poda). A poda da parte aérea foi realizada à altura de 15 cm em relação à superfície do solo. Foram avaliadas as seguintes características: produtividades de parte aérea, raiz e amido; porcentagem de massa seca e de amido e rendimento de farinha. As médias de variedades foram comparadas pelo teste Tukey e, para os intervalos entre podas, foi realizada análise de regressão. Foram utilizados contrastes para a comparação da testemunha com a média dos tratamentos podados. A variedade Caitité apresentou maior produtividade de raízes e maior produtividade de amido, compensando a redução no teor de massa seca de raízes que ocorreu com a poda. A poda influenciou negativamente a maioria das características avaliadas, entretanto, se realizada em intervalos a cada seis a oito meses, permite melhor distribuição da produção de parte aérea, sem promover elevada redução na produtividade de raízes tuberosas.

This experiment was conducted to evaluate the effect of pruning interval in two cassava varieties. The experiment was installed in the experimental area of Universidade Estadual do Sudoeste da Bahia, campus of Vitória da Conquista - BA, from December 2008 to July 2010, using a randomized complete block design, with ten treatments and three replications. Treatments were arranged in a 2x5 factorial design, formed by combining two varieties of cassava (Caitité and Sergipe) and five pruning intervals (two, four, six and eight months after planting and a witness - no pruning). The pruning was held at a height of 15 cm from the soil surface. Were evaluated the following characteristics: yields of shoot, root and starch; dry matter content, starch and flour yield. The average varieties were compared by Tukey test and for intervals between pruning, regression analysis. The variety Caitité had higher root yield and higher productivity starch, offsetting the reduction in the dry mass of roots that occurred with the pruning. Pruning negatively influenced most valued characteristics, however, was performed at intervals of every six to eight months, allows better distribution of production shoots, without promoting high reduction in root yield.