Designing the best breeding strategy for Coffea canephora: Genetic evaluation of pure and hybrid individuals aiming to select for productivity and disease resistance traits

Breeding programs of the species Coffea canephora rely heavily on the significant genetic variability between and within its two varietal groups (conilon and robusta). The use of hybrid families and individuals has been less common. The objectives of this study were to evaluate parents and families from the populations of conilon, robusta, and its hybrids and to define the best breeding and selection strategies for productivity and disease resistance traits. As such, 71 conilon clones, 56 robusta clones, and 20 hybrid families were evaluated over several years for the following traits: vegetative vigor, incidence of rust and cercosporiosis, fruit ripening time, fruit size, plant height, canopy diameter, and yield per plant. Components of variance and genetic parameters were estimated via residual maximum likelihood (REML) and genotypic values were predicted via best linear unbiased prediction (BLUP). Genetic variability among parents (clones) and hybrid families was detected for most of the evaluated traits. The Mulamba-Rank index suggests potential gains up to 17% for the genotypic aggregate of traits in the hybrid population. An intrapopulation recurrent selection within the hybrid population would be the best breeding strategy because the genetic variability, narrow and broad senses heritabilities and selective accuracies for important traits were maximized in the crossed population. Besides, such strategy is simple, low cost and quicker than the concurrent reciprocal recurrent selection in the two parental populations, and this maximizes the genetic gain for unit of time.

Resistance and Not Plant Fruit Traits Determine Root-Associated Bacterial Community Composition along a Domestication Gradient in Tomato

Soil bacterial communities are involved in multiple ecosystem services, key in determining plant productivity. Crop domestication and intensive agricultural practices often disrupt species interactions with unknown consequences for rhizosphere microbiomes. This study evaluates whether variation in plant traits along a domestication gradient determines the composition of root-associated bacterial communities; and whether these changes are related to targeted plant traits (e.g., fruit traits) or are side effects of less-often-targeted traits (e.g., resistance) during crop breeding. For this purpose, 18 tomato varieties (wild and modern species) differing in fruit and resistance traits were grown in a field experiment, and their root-associated bacterial communities were characterised. Root-associated bacterial community composition was influenced by plant resistance traits and genotype relatedness. When only considering domesticated tomatoes, the effect of resistance on bacterial OTU composition increases, while the effect due to phylogenetic relatedness decreases. Furthermore, bacterial diversity positively correlated with plant resistance traits. These results suggest that resistance traits not selected during domestication are related to the capacity of tomato varieties to associate with different bacterial groups. Taken together, these results evidence the relationship between plant traits and bacterial communities, pointing out the potential of breeding to affect plant microbiomes.

Whole-genome sequencing-based phylogeny, antibiotic resistance, and invasive phenotype of Escherichia coli strains colonizing the cervix of women in preterm labor

Background Escherichia coli is a major neonatal pathogen and the leading cause of early-onset sepsis in preterm newborns. Maternal E. coli strains are transmitted to the newborn causing invasive neonatal disease. However, there is a lack of data regarding the phenotypic and genotypic characterization of E. coli strains colonizing pregnant women during labor. Methods This prospective study performed at the University of Oklahoma Medical Center (OUHSC) from March 2014 to December 2015, aimed to investigate the colonization rate, and the phylogeny, antibiotic resistance traits, and invasive properties of E. coli strains colonizing the cervix of fifty pregnant women diagnosed with preterm labor (PTL). Molecular analyses including bacterial whole-genome sequencing (WGS), were performed to examine phylogenetic relationships among the colonizing strains and compare them with WGS data of representative invasive neonatal E. coli isolates. Phenotypic and genotypic antibiotic resistance traits were investigated. The bacteria’s ability to invade epithelial cells in vitro was determined. Results We recruited fifty women in PTL. Cervical samples yielded E. coli in 12 % (n=6). The mean gestational age was 32.5 (SD±3.19) weeks. None delivered an infant with E. coli disease. Phenotypic and genotypic antibiotic resistance testing did not overall demonstrate extensive drug resistance traits among the cervical E. coli isolates, however, one isolate was multi-drug resistant. The isolates belonged to five different phylogroups, and WGS analyses assigned each to individual multi-locus sequence types. Single nucleotide polymorphism-based comparisons of cervical E. coli strains with six representative neonatal E. coli bacteremia isolates demonstrated that only half of the cervical E. coli isolates were phylogenetically related to these neonatal invasive strains. Moreover, WGS comparisons showed that each cervical E. coli isolate had distinct genomic regions that were not shared with neonatal E. coli isolates. Cervical and neonatal E. coli isolates that were most closely related at the phylogenetic level had similar invasion capacity into intestinal epithelial cells. In contrast, phylogenetically dissimilar cervical E. coli strains were the least invasive among all isolates. Conclusions This pilot study showed that a minority of women in PTL were colonized in the cervix with E. coli, and colonizing strains were not phylogenetically uniformly representative of E. coli strains that commonly cause invasive disease in newborns. Larger studies are needed to determine the molecular characteristics of E. coli strains colonizing pregnant women associated with an increased risk of neonatal septicemia.

Comparison between methods for measuring fecal egg count and estimating genetic parameters for gastrointestinal parasite resistance traits in sheep

Fecal egg count (FEC) is an indicative measurement for parasite infection in sheep. Different FEC methods may show inconsistent results. Not accounting for inconsistencies can be problematic when integrating measurements from different FEC methods for genetic evaluation. The objectives of this study were to evaluate the difference in means and variances between two fecal egg counting methods used in sheep, the Modified McMaster (LMMR) and the Triple Chamber McMaster (LTCM); to estimate variance components for the two FEC methods, treating them as two different traits; and to integrate FEC data from the two different methods and estimate genetic parameters for FEC and other gastrointestinal parasite resistance traits. Fecal samples were collected from a commercial Rideau-Arcott sheep farm in Ontario. Fecal egg counting was performed using both Modified McMaster and the Triple Chamber McMaster methods. Other parasite resistance trait records were collected from the same farm including eye score (FAMACHA ©), body condition score (BCS), and body weight (WT). The two FEC methods were highly genetically (0.94) and phenotypically (0.88) correlated. However, the mean and variance between the two FEC methods were significantly different (P < 0.0001). Therefore, re-scaling is required prior to integrating data from the different methods. For the multiple trait analysis, data from the two fecal egg counting methods were integrated (LFEC) by using records for the LMMR when available and replacing missing records with re-standardized LTCM records converted to the same mean and variance of LMMR. Heritability estimates were 0.12 ± 0.04, 0.07 ± 0.05 , 0.17 ± 0.06, and 0.24 ± 0.07 for LFEC egg count, FAMACHA ©, BCS, and WT, respectively. The estimated genetic correlations between fecal egg count and the other parasite resistance traits were low and not significant (P>0.05) for FAMACHA © (r= 0.24 ± 0.32) and WT (r= 0.22 ± 0.19), and essentially zero for BCS (r= -0.03 ± 0.25), suggesting little to no benefit of using such traits as indicators for LFEC.

PSVIII-8 Genetic parameters for parasite resistance in an endangered and heritage sheep breed from Florida

The Florida Native Sheep is one of the oldest sheep breeds in the United States. This heritage breed from Florida, naturally adapted to humid and hot climate conditions, is one of the most parasite resistant breeds from the Southern US. However, only approximately 1,000 individuals remain alive in the world. Therefore, conservation efforts and breeding programs are critical for survival of this breed. The objective of this research was to estimate genetic parameters for parasite resistance and body condition score in Florida Native sheep. The pedigree file contained 695 animals born between 2018 and 2020 and included 279 individuals with genotypes (38,429 SNP after quality control). The dataset contained 365 animals with phenotypic records at 38 days post-infection (natural Haemonchus contortus infection) for fecal egg count (FEC), blood packed count volume (PCV), FAMACHA score (FAM), and body condition score (BCS). Genetic parameters were estimated using a multi-trait model with a Bayesian implementation in the GIBBS3F90 program. Heritabilities were 0.38 0.07, 0.47 0.05, 0.27 0.04, and 0.52 0.07 for FEC, PCV, FAM, and BCS. Genetic correlations among parasite resistance traits were high and favorable: -0.82 0.06 (FEC-PCV), 0.83 0.07 (FEC-FAM), and -0.94 0.03 (PCV-FAM). Genetic correlations among parasite resistance traits and BCS were -0.42 0.11 (FEC-BCS), 0.75 0.09 (PCV-BCS), and -0.82 0.05 (FAM-BCS). Genetic progress for parasite resistance is possible in Florida Native sheep. The FAMACHA score is a phenotypic parameter easy to record in sheep; therefore, genetic selection for this trait can be effective to improve the remaining traits.

Laccase Directed Lignification Is One of the Major Processes Associated With the Defense Response Against Pythium ultimum Infection in Apple Roots

Apple replant disease (ARD), incited by a pathogen complex including Pythium ultimum, causes stunted growth or death of newly planted trees at replant sites. Development and deployment of resistant or tolerant rootstocks offers a cost-effective, ecologically friendly, and durable approach for ARD management. Maximized exploitation of natural resistance requires integrated efforts to identify key regulatory mechanisms underlying resistance traits in apple. In this study, miRNA profiling and degradome sequencing identified major miRNA pathways and candidate genes using six apple rootstock genotypes with contrasting phenotypes to P. ultimum infection. The comprehensive RNA-seq dataset offered an expansive view of post-transcriptional regulation of apple root defense activation in response to infection from P. ultimum. Several pairs of miRNA families and their corresponding targets were identified for their roles in defense response in apple roots, including miR397-laccase, miR398-superoxide dismutase, miR10986-polyphenol oxidase, miR482-resistance genes, and miR160-auxin response factor. Of these families, the genotype-specific expression patterns of miR397 indicated its fundamental role in developing defense response patterns to P. ultimum infection. Combined with other identified copper proteins, the importance of cellular fortification, such as lignification of root tissues by the action of laccase, may critically contribute to genotype-specific resistance traits. Our findings suggest that quick and enhanced lignification of apple roots may significantly impede pathogen penetration and minimize the disruption of effective defense activation in roots of resistant genotypes. The identified target miRNA species and target genes consist of a valuable resource for subsequent functional analysis of their roles during interaction between apple roots and P. ultimum.

Rapid specialization of counter defenses enables two-spotted spider mite to adapt to novel plant hosts

Genetic adaptation, occurring over a long evolutionary time, enables host-specialized herbivores to develop novel resistance traits and to efficiently counteract the defenses of a narrow range of host plants. In contrast, physiological acclimation, leading to the suppression and/or detoxification of host defenses, is hypothesized to enable broad generalists to shift between plant hosts. However, the host adaptation mechanisms used by generalists composed of host-adapted populations are not known. Two-spotted spider mite (TSSM; Tetranychus urticae) is an extreme generalist herbivore whose individual populations perform well only on a subset of potential hosts. We combined experimental evolution, Arabidopsis thaliana genetics, mite reverse genetics, and pharmacological approaches to examine mite host adaptation upon the shift of a bean (Phaseolus vulgaris)-adapted population to Arabidopsis. We showed that cytochrome P450 monooxygenases are required for mite adaptation to Arabidopsis. We identified activities of two tiers of P450s: general xenobiotic-responsive P450s that have a limited contribution to mite adaptation to Arabidopsis and adaptation-associated P450s that efficiently counteract Arabidopsis defenses. In approximately 25 generations of mite selection on Arabidopsis plants, mites evolved highly efficient detoxification-based adaptation, characteristic of specialist herbivores. This demonstrates that specialization to plant resistance traits can occur within the ecological timescale, enabling the TSSM to shift to novel plant hosts.