Abstract
Soybean is important for protein and oil worldwide, requiring investments in research and production technology, mainly breeding programs, to meet the increasing demand. Seed morphology, ...including area, perimeter, and circularity, significantly impacts soybean yield. However, the analysis of these factors has been hindered by the lack of efficient computational approaches that offer accuracy and flexibility to user preferences and needs. This study presents a soybean phenotyping system framework that includes: seed segmentation in soybean images, morphological evaluation, and image‐based prediction of hundred‐seed weight (HSW). We used genotypes from a partial diallel cross design and collected red‐green‐blue images of seeds from each plot. We developed an in‐house image processing pipeline for seed segmentation, which enabled a full morphological evaluation of the seeds. For predicting the HSW, we compared machine learning algorithms using the obtained morphological characteristics as input and features from state‐of‐the‐art convolutional neural network (CNN) architectures. Our image segmentation methodology correctly identified over 98% of the seeds in the images, even when they were in proximity. Our morphological phenotyping approach's adaptability to other plant species was verified, fully demonstrating the pipeline's generalizability. The morphological measurements were effective in predicting the HSW with an accuracy of 0.71 predictive ability and mean squared error (MSE) of 3.15 (mean HSW of 19.74). The same results were observed for CNN features, highlighting the efficiency of the morphological measurements. ResNet‐50 had the most effective feature extraction, with a mean accuracy of 0.60 (MSE of 4.15). Our study can aid automated phenotyping tool development in research and industry.
Core Ideas
We introduce a novel high‐throughput soybean seed phenotyping system.
We demonstrate the possibility of predicting an important component of production for the soybean crop.
We show the efficiency of morphological measures as extractors of image features.
Our results indicate that ML techniques can be easily adapted to precision tasks in plant phenology.
ABSTRACT Stink bugs that affect soybeans are responsible for significant losses in seed production, quality and germination potential, in addition to hindering the mechanized harvest. To develop ...insect resistant materials, the breeder can compile a selection index by factor analysis. Therefore, the objective of this work was to validate the use of factor analysis, by means of its estimated gains, for the selection of highly productive and stink bugs resistant genotypes in two soybean segregating populations. For this, the phenotypic evaluation was performed in the generation F2:3, in two distinct experiments, being the populations from the crosses between IAC-100 × PI 295952 and IAC-100 × PI 306712. The experiments were installed in an 18 × 9 alpha-lattice design, with three replicates for each population. Agronomic and resistance characters were evaluated. The factorial scores for each character were obtained for the creation of “supercharacters”. These were designed to check if the selection in the new characters could provide satisfactory simultaneous gains in the original characters. Subsequently, the analysis of variance was performed for all factors, in both populations. The F test showed the presence of variability among genotypes, allowing the selection of superior genotypes. None of the factors selected progenies with all the characters favorably, and their use was not interesting for both populations. With this, complementary studies should be performed with other selection indices in these populations.
•Populations cultivated and managed for fruit production have high genetic diversity.•Managed populations have as high genetic diversity as protected populations.•Managed populations are genetically ...similar to protected populations.•Seeds extracted during pulp removal have high genetic variability.•Seeds extracted by fruit depulping can be used to recover overexploited populations.
The commercial exploitation of non-timber forest products (NTFPs) has been widely promoted to achieve both conservation and economic outcomes in the management of tropical forests by local communities, but monitoring the impacts of NTFPs harvesting is still challenging. Monitoring genetic diversity is a promising approach to assess harvesting impacts and guide best practices. Here, we evaluated the value of community-managed agroforests and secondary forests for conserving genetic structure and diversity of Euterpe edulis, an endemic palm explored for fruit and palm heart production. We used SSR markers to compare genetic diversity in populations growing in protected areas, in agroforests and in second-growth forests managed for fruit production in the coastal Atlantic Forest of Brazil. In addition, we investigated the genetic diversity of seeds extracted during pulp removal, which have been used in E. edulis reintroduction programs. Overall, high levels of genetic diversity were observed for all populations (mean allelic richness = 7.06; mean expected heterozygosity=0.787), with no significant differences in genetic diversity among agroforests, second-growth forests and protected areas. Managed forests and protected areas had low to intermediate levels of genetic differentiation (global Fixation Index=0.085), indicating the existence of gene flow among them. Seeds extracted during fruit pulp removal had as high genetic variability as populations growing in protected areas, thus evidencing the potential of using these seeds to recover overexploited populations. Thus, community-management of NTFPs in agroforests and second-growth forests may support genetic conservation of this threatened species, complementing the conservation role of protected areas.
The fall armyworm (FAW), Spodoptera frugiperda, is a significant pest of many crops in the world and it is native to the Americas, where the species has shown the ability to rapidly evolve resistance ...to insecticides and transgenic plants. Despite the importance of this species, there is a gap in the knowledge regarding the genetic structure of FAW in South America. Here, we examined the genetic diversity of FAW populations across a wide agricultural area of Brazil and Argentina using a Genotyping-by-Sequencing (GBS) approach. We also characterized samples by their host strain based on mitochondrial and Z-linked genetic markers. The GBS methodology enabled us to discover 3309 SNPs, including neutral and outlier markers. Data showed significant genetic structure between Brazil and Argentina populations, and also among the Argentinian ecoregions. Populations inside Brazil showed little genetic differentiation indicating high gene flow among locations and confirming that structure is related to the presence of corn and rice strains. Outlier analysis indicated 456 loci putatively under selection, including genes possibly related to resistance evolution. This study provides clarification of the population genetic structure of FAW in South America and highlights the importance of genomic research to understand the risks of spread of resistance genes.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Garlic is a spice and a medicinal plant; hence, there is an increasing interest in ‘developing’ new varieties with different culinary properties or with high content of nutraceutical compounds. ...Phenotypic traits and dominant molecular markers are predominantly used to evaluate the genetic diversity of garlic clones. However, 24 SSR markers (codominant) specific for garlic are available in the literature, fostering germplasm researches. In this study, we genotyped 130 garlic accessions from Brazil and abroad using 17 polymorphic SSR markers to assess the genetic diversity and structure. This is the first attempt to evaluate a large set of accessions maintained by Brazilian institutions. A high level of redundancy was detected in the collection (50 % of the accessions represented eight haplotypes). However, non-redundant accessions presented high genetic diversity. We detected on average five alleles per locus, Shannon index of 1.2, HO of 0.5, and HE of 0.6. A core collection was set with 17 accessions, covering 100 % of the alleles with minimum redundancy. Overall FST and D values indicate a strong genetic structure within accessions. Two major groups identified by both model-based (Bayesian approach) and hierarchical clustering (UPGMA dendrogram) techniques were coherent with the classification of accessions according to maturity time (growth cycle): early-late and midseason accessions. Assessing genetic diversity and structure of garlic collections is the first step towards an efficient management and conservation of accessions in genebanks, as well as to advance future genetic studies and improvement of garlic worldwide.
Knowledge about genetic diversity is essential to promote effective use and conservation of crops, because it enables farmers to adapt their crops to specific needs and is the raw material for ...breeding. Manioc (Manihot esculenta ssp. esculenta) is one of the world's major food crops and has the potential to help achieve food security in the context of on-going climate changes. We evaluated single nucleotide polymorphisms in traditional Brazilian manioc varieties conserved in the gene bank of the Luiz de Queiroz College of Agriculture, University of São Paulo. We assessed genome-wide diversity and identified selective signatures contrasting varieties from different biomes with samples of manioc's wild ancestor M. esculenta ssp. flabellifolia. We identified signatures of selection putatively associated with resistance genes, plant development and response to abiotic stresses that might have been important for the crop's domestication and diversification resulting from cultivation in different environments. Additionally, high neutral genetic diversity within groups of varieties from different biomes and low genetic divergence among biomes reflect the complexity of manioc's evolutionary dynamics under traditional cultivation. Our results exemplify how smallholder practices contribute to conserve manioc's genetic resources, maintaining variation of potential adaptive significance and high levels of neutral genetic diversity.
The analysis of the genetic diversity of ginger based on agronomic traits is essential to know its performance and to design breeding programs. In this study, we analyzed the phenotypic variability ...of 61 accessions of the ginger germplasm collection of the "Luiz de Queiroz" College of Agriculture at the University of Sao Paulo (ESALQ/USP) in a complete randomized block design with four replications. An analysis of variance test was performed and genetic parameters such as heritability, genetic variance, environmental variance, genetic-environmental variation ratio (CVg/CVe) and genetic correlations were estimated. There were highly significant differences (P≤0.01) among the accessions for all the agronomic traits analyzed. The CVg/CVe ratio (>1), along with the high heritability (>80%), showed a significant contribution of genetic factors on the phenotypic expression of plant height, rhizome thickness and yield traits, favoring the clonal selection of genotypes. Accessions Gen-29, Gen-29, Gen-32, Gen-36, Gen-37, Gen-40, Gen-41, Gen-42, Gen-50 were selected due to the best agronomic performance when compared to the rest of the germplasm. The results obtained may be useful in future breeding programs in Brazil.
Ginger is a vegetable with medicinal and culinary properties widely cultivated in the Southern and Southeastern Brazil. The knowledge of ginger species’ genetic variability is essential to direct ...correctly future studies of conservation and genetic improvement, but in Brazil, little is known about this species’ genetic variability. In this study, we analyzed the genetic diversity and structure of 55 Brazilian accessions and 6 Colombian accessions of ginger, using AFLP (
Amplified Fragment Length Polymorphism
) molecular markers. The molecular characterization was based on 13 primers combinations, which generated an average of 113.5 polymorphic loci. The genetic diversity estimates of Nei (
Hj
), Shannon–Weiner index (
I
) and an effective number of alleles (
n
e
) were greater in the Colombian accessions in relation to the Brazilian accessions. The analysis of molecular variance showed that most of the genetic variation occurred between the two countries while in the Brazilian populations there is no genetic structure and probably each region harbors 100 % of genetic variation found in the samples. The bayesian model-based clustering and the dendrogram using the dissimilarity’s coefficient of Jaccard were congruent with each other and showed that the Brazilian accessions are highly similar between themselves, regardless of the geographic region of origin. We suggested that the exploration of the interspecific variability and the introduction of new varieties of
Z.officinale
are viable alternatives for generating diversity in breeding programs in Brazil. The introduction of new genetic materials will certainly contribute to a higher genetic basis of such crop.
PDF
