breeding programs
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2023 ◽  
Vol 83 ◽  
B. R. R. M. Nassau ◽  
P. S. C. Mascarenhas ◽  
A. G. Guimarães ◽  
F. M. Feitosa ◽  
H. M. Ferreira ◽  

Abstract The inheritance of the seedless fruit characteristic of Annona squamosa has not yet been explained. Molecular techniques may aid breeding programs, mainly in the assisted selection of the target gene. The INO gene may be related to seed development in these fruits. The objective of the present paper was to investigate the inheritance of seedlessness in the 'Brazilian seedless' sugar apple and INO gene conservation in Annona squamosa and Annona cherimola x Annona squamosa genotypes by assessing their homology with the INO database genes. The F1 generation was obtained by crossing the mutant 'Brazilian seedless' (male genitor) (P1) with the wild-type A. squamosa with seeds (M1 and M2, female genitors). The INO gene was studied in mutant and wild-type A. squamosa (P1, M1, M2 and M3) and in the Gefner atemoya (A. cherimola x A. squamosa) (M4) cultivar. The DNA was extracted from young leaves, and four sets of specific primers flanking the INO gene were amplified. The seedless characteristic was identified as stenospermatic in the fruits of parental P1, suggesting monogenic inheritance with complete dominance. High sequence similarity of the INO gene amplifications in the sugar apple accessions (M1, M2, M3) and the atemoya cultivar Gefner (M4) reinforces the hypothesis of their conservation.

2022 ◽  
Vol 3 (1) ◽  
Xuechun Bai ◽  
Graham S. Plastow

AbstractDisease resilience, defined as an animal’s ability to maintain productive performance in the face of infection, provides opportunities to manage the polymicrobial challenge common in pig production. Disease resilience can deliver a number of benefits, including more sustainable production as well as improved animal health and the potential for reduced antimicrobial use. However, little progress has been made to date in the application of disease resilience in breeding programs due to a number of factors, including (1) confusion around definitions of disease resilience and its component traits disease resistance and tolerance, and (2) the difficulty in characterizing such a complex trait consisting of multiple biological functions and dynamic elements of rates of response and recovery from infection. Accordingly, this review refines the definitions of disease resistance, tolerance, and resilience based on previous studies to help improve the understanding and application of these breeding goals and traits under different scenarios. We also describe and summarize results from a “natural disease challenge model” designed to provide inputs for selection of disease resilience. The next steps for managing polymicrobial challenges faced by the pig industry will include the development of large-scale multi-omics data, new phenotyping technologies, and mathematical and statistical methods adapted to these data. Genome editing to produce pigs resistant to major diseases may complement selection for disease resilience along with continued efforts in the more traditional areas of biosecurity, vaccination and treatment. Altogether genomic approaches provide exciting opportunities for the pig industry to overcome the challenges provided by hard-to-manage diseases as well as new environmental challenges associated with climate change.

BMC Genomics ◽  
2022 ◽  
Vol 23 (1) ◽  
Sirlene Viana de Faria ◽  
Leandro Tonello Zuffo ◽  
Wemerson Mendonça Rezende ◽  
Diego Gonçalves Caixeta ◽  
Hélcio Duarte Pereira ◽  

Abstract Background The characterization of genetic diversity and population differentiation for maize inbred lines from breeding programs is of great value in assisting breeders in maintaining and potentially increasing the rate of genetic gain. In our study, we characterized a set of 187 tropical maize inbred lines from the public breeding program of the Universidade Federal de Viçosa (UFV) in Brazil based on 18 agronomic traits and 3,083 single nucleotide polymorphisms (SNP) markers to evaluate whether this set of inbred lines represents a panel of tropical maize inbred lines for association mapping analysis and investigate the population structure and patterns of relationships among the inbred lines from UFV for better exploitation in our maize breeding program. Results Our results showed that there was large phenotypic and genotypic variation in the set of tropical maize inbred lines from the UFV maize breeding program. We also found high genetic diversity (GD = 0.34) and low pairwise kinship coefficients among the maize inbred lines (only approximately 4.00 % of the pairwise relative kinship was above 0.50) in the set of inbred lines. The LD decay distance over all ten chromosomes in the entire set of maize lines with r2 = 0.1 was 276,237 kb. Concerning the population structure, our results from the model-based STRUCTURE and principal component analysis methods distinguished the inbred lines into three subpopulations, with high consistency maintained between both results. Additionally, the clustering analysis based on phenotypic and molecular data grouped the inbred lines into 14 and 22 genetic divergence clusters, respectively. Conclusions Our results indicate that the set of tropical maize inbred lines from UFV maize breeding programs can comprise a panel of tropical maize inbred lines suitable for a genome-wide association study to dissect the variation of complex quantitative traits in maize, mainly in tropical environments. In addition, our results will be very useful for assisting us in the assignment of heterotic groups and the selection of the best parental combinations for new breeding crosses, mapping populations, mapping synthetic populations, guiding crosses that target highly heterotic and yielding hybrids, and predicting untested hybrids in the public breeding program UFV.

PLoS ONE ◽  
2022 ◽  
Vol 17 (1) ◽  
pp. e0262309
Muhammad Haseeb ◽  
Shahid Iqbal ◽  
Muhammad Bilal Hafeez ◽  
Muhammad Sohail Saddiq ◽  
Noreen Zahra ◽  

The amount of soil contaminated with heavy metal increases due to urbanization, industrialization, and anthropogenic activities. Quinoa is considered a useful candidate in the remediation of such soil. In this pot experiment, the phytoextraction capacity of quinoa lines (A1, A2, A7, and A9) against different nickel (Ni) concentrations (0, 50, and 100 mg kg-1) were investigated. Required Ni concentrations were developed in polythene bags filled with sandy loam soil using nickel nitrate salt prior to two months of sowing and kept sealed up to sowing. Results showed that translocation of Ni increased from roots to shoots with an increase in soil Ni concentration in all lines. A2 line accumulated high Ni in leaf compared to the root as depicted by translocation factor 3.09 and 3.21 when grown at soil having 50 and 100 Ni mg kg-1, respectively. While, in the case of root, A7 accumulated high Ni followed by A9, A1, and A2, respectively. There was a 5–7% increased seed yield by 50 mg kg-1 Ni in all except A1 compared to control. However, growth and yield declined with a further increase in Ni level. The maximum reduction in yield was noticed in A9, which was strongly linked with poor physiological performance, e.g., chlorophyll a, b, and phenolic contents. Ni concentrations in the seed of all lines were within the permissible value set (67 ppm) by FAO/WHO. The result of the present study suggests that quinoa is a better accumulator of Ni. This species can provide the scope of decontamination of heavy metal polluted soil. The screened line can be used for future quinoa breeding programs for bioremediation and phytoextraction purpose.

2022 ◽  
Vol 12 ◽  
Paul Galewski ◽  
Andrew Funk ◽  
J. Mitchell McGrath

Understanding the genetic basis of polygenic traits is a major challenge in agricultural species, especially in non-model systems. Select and sequence (SnS) experiments carried out within existing breeding programs provide a means to simultaneously identify the genomic background of a trait while improving the mean phenotype for a population. Using pooled whole genome sequencing (WGS) of selected and unselected bulks derived from a synthetic outcrossing sugar beet population EL57 (PI 663212), which segregates for seedling rhizoctonia resistance, we identified a putative genomic background involved in conditioning a resistance phenotype. Population genomic parameters were estimated to measure fixation (He), genome divergence (FST), and allele frequency changes between bulks (DeltaAF). We report on the genome wide patterns of variation resulting from selection and highlight specific genomic features associated with resistance. Expected heterozygosity (He) showed an increased level of fixation in the resistant bulk, indicating a greater selection pressure was applied. In total, 1,311 biallelic loci were detected as significant FST outliers (p < 0.01) in comparisons between the resistant and susceptible bulks. These loci were detected in 206 regions along the chromosomes and contained 275 genes. We estimated changes in allele frequency between bulks resulting from selection for resistance by leveraging the allele frequencies of an unselected bulk. DeltaAF was a more stringent test of selection and recovered 186 significant loci, representing 32 genes, all of which were also detected using FST. Estimates of population genetic parameters and statistical significance were visualized with respect to the EL10.2 physical map and produced a candidate gene list that was enriched for function in cell wall metabolism and plant disease resistance, including pathogen perception, signal transduction, and pathogen response. Specific variation associated with these genes was also reported and represents genetic markers for validation and prediction of resistance to Rhizoctonia. Select and sequence experiments offer a means to characterize the genetic base of sugar beet, inform selection within breeding programs, and prioritize candidate variation for functional studies.

Plant Disease ◽  
2022 ◽  
Francisco Beluzán ◽  
Xavier Miarnau ◽  
Laura Torguet ◽  
Lourdes Zazurca ◽  
Paloma Abad-Campos ◽  

Twenty-five almond cultivars were assessed for susceptibility to Diaporthe amygdali, causal agent of twig canker and shoot blight disease. In laboratory experiments, growing twigs were inoculated with four D. amygdali isolates. Moreover, growing shoots of almond cultivars grafted onto INRA ‘GF-677’ rootstock were used in four-year field inoculations with one D. amygdali isolate. In both type of experiments, inoculum consisted of agar plugs with mycelium, which were inserted underneath the bark and the lesion lengths caused by the fungus were measured. Necrotic lesions were observed in the inoculated almond cultivars both in laboratory and field tests, confirming the susceptibility of all the evaluated cultivars to all the inoculated isolates of D. amygdali. Cultivars were grouped as susceptible or very susceptible according to a cluster analysis. The relationship between some agronomic traits and cultivar susceptibility was also investigated. Blooming and ripening times were found relevant variables to explain cultivars performance related to D. amygdali susceptibility. Late and very late blooming, and early and medium ripening cultivars were highly susceptible to D. amygdali. Our results may provide valuable information that could assist in ongoing breeding programs of this crop and additionally in the selection of cultivars for new almond plantations.

2022 ◽  
Irene S. Breider ◽  
R. Chris Gaynor ◽  
Gregor Gorjanc ◽  
Steve Thorn ◽  
Manish K. Pandey ◽  

Abstract Some of the most economically important traits in plant breeding show highly polygenic inheritance. Genetic variation is a key determinant of the rates of genetic improvement in selective breeding programs. Rapid progress in genetic improvement comes at the cost of a rapid loss of genetic variation. Germplasm available through expired Plant Variety Protection (exPVP) lines is a potential resource of variation previously lost in elite breeding programs. Introgression for polygenic traits is challenging, as many genes have a small effect on the trait of interest. Here we propose a way to overcome these challenges with a multi-part pre-breeding program that has feedback pathways to optimise recurrent genomic selection. The multi-part breeding program consists of three components, namely a bridging component, population improvement, and product development. Parameters influencing the multi-part program were optimised with the use of a grid search. Haploblock effect and origin were investigated. Results showed that the introgression of exPVP germplasm using an optimised multi-part breeding strategy resulted in 1.53 times higher genetic gain compared to a two-part breeding program. Higher gain was achieved through reducing the performance gap between exPVP and elite germplasm and breaking down linkage drag. Both first and subsequent introgression events showed to be successful. In conclusion, the multi-part breeding strategy has a potential to improve long-term genetic gain for polygenic traits and therefore, potential to contribute to global food security.

Animals ◽  
2022 ◽  
Vol 12 (2) ◽  
pp. 174
Gerardo Alves Fernandes Júnior ◽  
Delvan Alves Silva ◽  
Lucio Flavio Macedo Mota ◽  
Thaise Pinto de Melo ◽  
Larissa Fernanda Simielli Fonseca ◽  

Increasing productivity through continued animal genetic improvement is a crucial part of implementing sustainable livestock intensification programs. In Zebu cattle, the lack of sexual precocity is one of the main obstacles to improving beef production efficiency. Puberty-related traits are complex, but large-scale data sets from different “omics” have provided information on specific genes and biological processes with major effects on the expression of such traits, which can greatly increase animal genetic evaluation. In addition, genetic parameter estimates and genomic predictions involving sexual precocity indicator traits and productive, reproductive, and feed-efficiency related traits highlighted the feasibility and importance of direct selection for anticipating heifer reproductive life. Indeed, the case study of selection for sexual precocity in Nellore breeding programs presented here show that, in 12 years of selection for female early precocity and improved management practices, the phenotypic means of age at first calving showed a strong decreasing trend, changing from nearly 34 to less than 28 months, with a genetic trend of almost −2 days/year. In this period, the percentage of early pregnancy in the herds changed from around 10% to more than 60%, showing that the genetic improvement of heifer’s sexual precocity allows optimizing the productive cycle by reducing the number of unproductive animals in the herd. It has a direct impact on sustainability by better use of resources. Genomic selection breeding programs accounting for genotype by environment interaction represent promising tools for accelerating genetic progress for sexual precocity in tropical beef cattle.

Forests ◽  
2022 ◽  
Vol 13 (1) ◽  
pp. 106
Dalina Rodríguez-Pérez ◽  
Róger Moya ◽  
Olman Murillo ◽  
Johana Gaitán-Álvarez ◽  
Yorleny Badilla-Valverde

The Dipteryx genus has a natural distribution throughout several tropical countries in Latin America. This taxon has several tree species, all recognized for their high-density wood. The objective of this research was to study the variation and genetic control of several wood properties, including bark, sapwood, heartwood, green density (GD), specific gravity (SG), moisture content in green condition (MC-G), and mechanical properties, in a Dipteryx panamensis provenance/progeny test at 8 years old. The results showed that bark varied little among families and provenances, but heartwood (diameter and percentage) showed high genetic variation. SG and MC-G showed significant variation between provenances and families, while GD showed little variation. Among the mechanical properties evaluated, the greatest genetic variation was observed in the MOR in bending and shear stress. Families from the Coope San Juan provenance registered the highest values in all wood properties investigated, and families from Puerto Viejo obtained the lowest. Family heritability and the coefficient of genetic variation exhibited high values in heartwood/sapwood and the MOR in bending (h2 > 0.9 and CV > 20%) and lower values in SG, MC-G, compression stress, and shear stress. D. panamensis wood properties have a high potential to be improved through breeding programs.

2022 ◽  
Vol 12 ◽  
Jing Zhou ◽  
Eduardo Beche ◽  
Caio Canella Vieira ◽  
Dennis Yungbluth ◽  
Jianfeng Zhou ◽  

The efficiency of crop breeding programs is evaluated by the genetic gain of a primary trait of interest, e.g., yield, achieved in 1 year through artificial selection of advanced breeding materials. Conventional breeding programs select superior genotypes using the primary trait (yield) based on combine harvesters, which is labor-intensive and often unfeasible for single-row progeny trials (PTs) due to their large population, complex genetic behavior, and high genotype-environment interaction. The goal of this study was to investigate the performance of selecting superior soybean breeding lines using image-based secondary traits by comparing them with the selection of breeders. A total of 11,473 progeny rows (PT) were planted in 2018, of which 1,773 genotypes were selected for the preliminary yield trial (PYT) in 2019, and 238 genotypes advanced for the advanced yield trial (AYT) in 2020. Six agronomic traits were manually measured in both PYT and AYT trials. A UAV-based multispectral imaging system was used to collect aerial images at 30 m above ground every 2 weeks over the growing seasons. A group of image features was extracted to develop the secondary crop traits for selection. Results show that the soybean seed yield of the selected genotypes by breeders was significantly higher than that of the non-selected ones in both yield trials, indicating the superiority of the breeder's selection for advancing soybean yield. A least absolute shrinkage and selection operator model was used to select soybean lines with image features and identified 71 and 76% of the selection of breeders for the PT and PYT. The model-based selections had a significantly higher average yield than the selection of a breeder. The soybean yield selected by the model in PT and PYT was 4 and 5% higher than those selected by breeders, which indicates that the UAV-based high-throughput phenotyping system is promising in selecting high-yield soybean genotypes.

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