Half-sib Families Research Articles

Divergent selection predating the Last Glacial Maximum mainly acted on macro-phenotypes in Norway spruce.

The current distribution and population structure of many species were, to a large extent, shaped by cycles of isolation in glacial refugia and subsequent population expansions. Isolation in and postglacial expansion through heterogeneous environments led to either neutral or adaptive divergence. Norway spruce is no exception, and its current distribution is the consequence of a constant interplay between evolutionary and demographic processes. We investigated population differentiation and adaptation of Norway spruce for juvenile growth, diameter of the stem, wood density, and tracheid traits at breast height. Data from 4461 phenotyped and genotyped Norway spruce from 396 half-sib families in two progeny tests were used to test for divergent selection in the framework of Q ST vs. F ST. We show that the macroscopic resultant trait (stem diameter), unlike its microscopic components (tracheid dimensions) and juvenile growth, was under divergent selection that predated the Last Glacial Maximum. Altogether, the current variation in these phenotypic traits in Norway spruce is better explained by local adaptation to ancestral environments than to current ones, where populations were partly preadapted, mainly through growth-related traits.

Weighted kernels improve multi-environment genomic prediction

Crucial to variety improvement programs is the reliable and accurate prediction of genotype’s performance across environments. However, due to the impactful presence of genotype by environment (G×E) interaction that dictates how changes in expression and function of genes influence target traits in different environments, prediction performance of genomic selection (GS) using single-environment models often falls short. Furthermore, despite the successes of genome-wide association studies (GWAS), the genetic insights derived from genome-to-phenome mapping have not yet been incorporated in predictive analytics, making GS models that use Gaussian kernel primarily an estimator of genomic similarity, instead of the underlying genetics characteristics of the populations. Here, we developed a GS framework that, in addition to capturing the overall genomic relationship, can capitalize on the signal of genetic associations of the phenotypic variation as well as the genetic characteristics of the populations. The capacity of predicting the performance of populations across environments was demonstrated by an overall gain in predictability up to 31% for the winter wheat DH population. Compared to Gaussian kernels, we showed that our multi-environment weighted kernels could better leverage the significance of genetic associations and yielded a marked improvement of 4–33% in prediction accuracy for half-sib families. Furthermore, the flexibility incorporated in our Bayesian implementation provides the generalizable capacity required for predicting multiple highly genetic heterogeneous populations across environments, allowing reliable GS for genetic improvement programs that have no access to genetically uniform material.

Genetic Resistance of Switchgrass to Rust Evaluated in a Composite Upland × Lowland Population in Lab and Field Settings

Maintaining low levels of rust incidence (caused by Puccinia novopanici) in switchgrass (Panicum virgatum L.) breeding populations is a priority for the USDA-ARS program engaged in improving cultivars for high biomass yield and quality. Essential to this goal is the unbiased and accurate estimation of genetic parameters to predict the merits of parents and progeny. Spores of the fungus were inoculated in greenhouse-grown seedling progeny of 31 half-sib families in generation 2 (Gen 2) of a composite Summer × Kanlow population for evaluation of rust incidence on the leaves with a 0–9 rating scale. Two parents were later chosen to cross and develop a linkage mapping population as Gen 3. The Gen 2, 3, and Kanlow seedlings were transplanted into the field located near Mead, NE, in early June 2020 and laid out as a replicated row–column design with six blocks of single-row plots of five plants each. The field trial was rated in September 2021 and 2022 with a 0–4 scale. Lab and field data were subjected to univariate linear mixed models via the restricted maximum likelihood to extract the variance components needed to predict the breeding values. The additive genetic variation was substantial (p < 0.01), enough to result in high heritability estimates ranging from 0.42 ± 14 to 0.73 ± 0.09 at the individual and family mean levels. This result implies that rust resistance is under strong genetic control to use mass selection for obtaining satisfactory gains. A possible rust incidence x year interaction was detected with a Spearman correlation of breeding values of −0.38, caused by significant rank changes of the Gen 3 genotypes in 2022 (a high heat and drought year). Genetic gains were predicted to reduce rust incidence scores by at least two points on the rating scale when selecting backwards, and by one point when selecting individual candidates as parents of the next generation. Faster gains (31 and 59%) were realized relative to the second generation by respectively selecting the top 10% of the families in Gen 3 or the top 10% of genotypes within this group. Based on these results, strategies for controlling the incidence of rust will be developed to optimize gains in the other traits of economic importance.

Viabilidade da visão computacional no melhoramento genético na produção de raízes de batata-doce

ABSTRACT The improvement of sweet potato is a costly job due to the large number of characteristics to be analyzed for the selection of the best genotypes, making it necessary to adopt new technologies, such as the use of images, associated with the phenotyping process. The objective of this research was to develop a methodology for the phenotyping of the root production aiming genetic improvement of half-sib sweet potato progenies through computational analysis of images and to compare its performance to the traditional methodology of evaluation. Sixteen half-sib sweet potato families in a randomized block design with 4 replications were evaluated. At plant level, the weight per root and the total number of roots were evaluated. The images were acquired in a “studio” made of mdf with a digital camera model Canon PowerShotSX400 IS, under artificial lighting. The evaluations were carried out using the R software, where a second-degree polynomial regression model was fitted to predict the root weight (in grams) and the genetic values and expected gains were obtained. It was possible to predict the root weight at plant and plot level, obtaining high coefficients of determination between the predicted and observed weight. Computer vision allowed the prediction of root weight, maintaining the genotype ranking and consequently the similarity between the expected gains with the selection. Thus, the use of images is an efficient tool for sweet potato genetic improvement programs, assisting in the crop phenotyping process.

Drought Resistance Evaluation of Casuarina equisetifolia Half-Sib Families at the Seedling Stage and the Response of Five NAC Genes to Drought Stress

Casuarina equisetifolia (L.) is an indispensable tree species in the construction of the backbone of the shelterbelt system in subtropical coastal regions, as it can resist wind, sand, drought, and salt. Under global warming and water shortage, it is important to clarify the mechanisms through which C. equisetifolia adapts to drought stress and to breed drought-resistant varieties in order to enhance the ecological protection provided by coastal shelterbelts. Here, we aimed to explore the response characteristics of C. equisetifolia to drought stress and investigate the associations of NAC genes with drought resistance. Seedlings of 16 half-sib C. equisetifolia families were subjected to drought treatment. Seedling growth, morphology, physiological and biochemical indices, and drought resistance were comprehensively evaluated. The drought-resistant families designated 4-383, 3-80, 3-265, 3-224, and 1-195 were selected using multiple indices and methods. Correlation and structural equation model analyses revealed that CCG007578 might regulate growth and osmoprotection in C. equisetifolia while CCG028838 and CCG004029 may scavenge reactive oxygen species. The correlation and structural equation model analyses of seedling height growth (ΔH), survival rate (S), malondialdehyde (MDA), superoxide dismutase (SOD), and CCG007578 expression were used to identify drought resistance in C. equisetifolia. The aforementioned drought-resistant families provide basic materials for future research on genes encoding drought-resistance proteins and the molecular breeding of drought-resistant C. equisetifolia.

Genetic analysis and physiological relationships of drought response in fennel: Interaction with mating system.

The consequences of water deficit and its interaction with pollination system (deliberate selfing compared with open-pollination) on physiological, agronomic and phytochemical traits are not understood in fennel (Foeniculum vulgare Mill.). A research was started by creating selfed (S1) and half-sib (HS) families on a fennel germplasm in 2018. Populations were studied in the field, applying a normal and a water deficit condition during two years (2019-2020). Considerable genotypic variation was observed within S1 and HS families for all of the evaluated traits, demonstrating that selection for these traits would be successful. Consequences of water deficit were manifested as declined most of the traits; and significantly increased essential oil content, harvest index, and proline content, in both populations. Mandatory selfing reduced the performance of genotypes for most of the traits confirming the existence of inbreeding depression (ID) with higher values for plant dry weight, seed yield, essential oil content, and number of umbelets per umbel. In S1 population, some of the studied traits had higher heritability estimates under normal condition and some of them showed higher heritability under water deficit. Positive relationship between GCA and STI in OP population indicated that it is possible to identify genotypes having high values of combining ability and drought tolerance. Results of the present study suggest that physiological traits cannot be used as an indicator to distinguish drought-tolerant genotypes in S1 progenies, whereas in OP progenies Chl a, Chl b, TChl, CAR, PRO, and RWC, which had significant correlations with drought tolerance, may be used for this purpose. Based on the results contrasting genotypes were identified, which can be used to develop mapping populations for genome studies of drought tolerance and physiological traits of this species in future studies.

Transcriptome and metabolome analyses of lignin biosynthesis mechanism of Platycladus orientalis.

Platycladus orientalis, as an important plant for ecological protection, is a pioneer tree species for afforestation in arid and barren mountainous areas. Lignin has the functions of water and soil conservation, strengthening plant mechanical strength and resisting adverse environmental effects and plays an important role in the ecological protection benefits of P. orientalis. In this study, annual dynamic observations of the lignin content in roots, stems and leaves of one-year-old seedlings of a P. orientalis half-sib family were carried out, and combined transcriptome and metabolome analyses were carried out during three key stages of P. orientalis stem development. The lignin contents in roots, stems and leaves of P. orientalis showed extremely significant spatiotemporal differences. In the stems, lignin was mainly distributed in the cell walls of the pith, xylem, phloem, pericyte, and epidermis, with differences in different periods. A total of 226 metabolites were detected in the stem of P. orientalis, which were divided into seven categories, including 10 synthetic precursor compounds containing lignin. Among them, the content of coniferyl alcohol was the highest, accounting for 12.27% of the total content, and caffeyl alcohol was the lowest, accounting for 7.05% only. By annotating the KEGG functions, a large number of differentially expressed genes and differential metabolites were obtained for the comparison combinations, and seven key enzymes and 24 related genes involved in the process of lignin synthesis in P. orientalis were selected. Based on the results of the metabolic mechanism of lignin in P. orientalis by biochemical, anatomical and molecular biological analyzes, the key regulatory pathways of lignin in P. orientalis were identified, which will be of great significance for regulating the lignin content of P. orientalis and improving the adaptability and resistance of this plant.

Heritability of dispersal-related larval traits in the clown anemonefish Amphiprion percula.

A major goal of marine ecology is to identify the drivers of variation in larval dispersal. Larval traits are emerging as an important potential source of variation in dispersal outcomes, but little is known about how the evolution of these traits might shape dispersal patterns. Here, we consider the potential for adaptive evolution in two possibly dispersal-related traits by quantifying the heritability of larval size and swimming speed in the clown anemonefish (Amphiprion percula). Using a laboratory population of wild-caught A. percula, we measured the size and swimming speed of larvae from 24 half-sibling families. Phenotypic variance was partitioned into genetic and environmental components using a linear mixed-effects model. Importantly, by including half-siblings in the breeding design, we ensured that our estimates of genetic variance do not include nonheritable effects shared by clutches of full-siblings, which could lead to significant overestimates of heritability. We find unequivocal evidence for the heritability of larval body size (estimated between 0.21 and 0.34) and equivocal evidence for the heritability of swimming speed (between 0.05 and 0.19 depending on the choice of prior). From a methodological perspective, this work demonstrates the importance of evaluating sensitivity to prior distribution in Bayesian analysis. From a biological perspective, it advances our understanding of potential dispersal-related larval traits by quantifying the extent to which they can be inherited and thus have the potential for adaptive evolution.

Age–age correlations and efficiency of early selection for growth traits and inner shell color parameters in a golden strain of Hyriopsis cumingii

Hyriopsis cumingii is the most important freshwater mussel for pearl production in China, however, early selection for growth traits and inner shell color in this species is poorly characterized. To explore the optimal selection age, the growth traits (SW, SH, SL, and BW) and inner shell color parameters (L*, a*, b* and dE*) of 22 half-sib families were measured at the ages of 5, 12, and 17 months in a progeny test population established at the Weimin Aquaculture Company breeding base, Zhejiang Province, China. The phenotypic data for growth traits and inner shell color parameters were divided into breeding (50% growth traits × 50% shell color traits)and control groups and were analyzed. Age–age genetic and phenotypic correlations, and heritability were also examined. The results showed significant differences in growth traits between the two groups as age increased (P < 0.05). The b* values in the breeding group were considerably higher than those in the control group and the difference between the two groups was highly significant at all the tested ages (P < 0.01). The growth traits and inner shell color parameters had a moderate to high heritability (h2 ≥ 0.15) at all ages and b* values reached 0.44 at 5 months of age. The age–age genetic and phenotypic correlations of growth traits were always positive, ranging from 0.224 to 0.933 and 0.087 to 0.615, respectively. The age–age genetic and phenotypic correlations of the inner shell color parameters were also always positive, ranging from 0.224 to 0.954 and 0.097 to 0.816, respectively. The results of this study can be used to assist in the early selection practices for the selective breeding of H. cumingii's golden strain. For the early selection of growth traits and inner shell color, SH and b* are preferable, respectively, as target traits.

Recurrent selection of new breeding lines and yield potential, nutrient profile and in vitro rumen characteristics of Melilotus officinalis

Melilotus officinalis is an important forage and green manure crop. There is a high degree of genetic diversity within species of M. officinalis . Despite the forage potential and the ability of nitrogen fixation, it has not been propagated in recent years because its high coumarin content. As a forage crop, the breeding goal of M. officinalis was mainly focused on improving forage yield and quality and reducing coumarin content. In this study, 25 superior half sib (HS) families of M. officinalis were used to carry out the second cycle recurrent selection, and genotypic variation of key traits (yield, quality and coumarin content) at two locations during 2018 and 2019 seasons were evaluated. Significant genotypic variation existed for the key traits: plant height (PH), dry biomass (DB), crude protein (CP), acid detergent fiber, neutral detergent fiber and coumarin. Also, significant genotype × location interactions were observed for the traits: DB, PH, CP, stem diameter, acid detergent lignin and acid insoluble ash ( P < 0.05). Coumarin was negatively correlated with DB and PH, and positively correlated with CP. Genetic gain of all the traits of the second cycle recurrent selection were lower than that of the first cycle recurrent selection, except for PH and leaf/stem ratio (LSR). After the second cycle recurrent selection, the genetic gains of coumarin and LSR were higher than for other traits. Furthermore, new breeding lines generated by polycrossing superior HS families were evaluated. The polycrossing improved the yield and in vitro rumen fermentation characteristics and reduced the coumarin content. Our work provides new breeding lines of M. officinalis, beneficial for a sustainable grassland-based livestock industry. • Genotype × environment interactions affect yield and quality traits. • Recurrent selection process is useful to obtain plant materials with low coumarin content and high yield. • Superiority of new M. officinalis lines over currently grown demonstrated on fields and in vitro rumen fermentation. • We developed new breeding lines of M. officinalis beneficial for livestock industry.

Comprehensive selection and variation analysis of growth traits and wood color of Castanopsis hystrix half-sib families

Comprehensive selection and variation analysis of growth traits and wood color of Castanopsis hystrix half-sib families

Growth performance and G × E interactions of Liriodendron tulipifera half-sib families across ages in eastern China

Growth performance and G × E interactions of Liriodendron tulipifera half-sib families across ages in eastern China

Sawn-timber quality of six half-sib families of hinoki cypress (Chamaecyparis obtusa (Siebold et Zucc.) Endl.)

ABSTRACT To clarify sawn-timber quality and those among-family variations of hinoki cypress (Chamaecyparis obtusa), modulus of elasticity (MOE) and modulus of rupture (MOR) were evaluated for 97 pieces of 38 by 89 mm sawn timber produced from half-sib families planted in a progeny test stand at Chiba, Japan. Correlations were evaluated on mechanical properties in standing trees and logs with MOE and MOR in the sawn timber. Elastic properties, such as dynamic Young’s modulus of logs and MOE, were affected by genetic factors compared with air-dry density and MOR. The 5% tolerance limits at a 75% confidence level (f 0.05) of MOE and MOR were 8.03 GPa and 39.4 MPa, respectively. The f 0.05 values of MOR exceeded the characteristic value of the sawn timber in visual grading class SS of Japanese Agricultural Standard for the JS-I. Visual grading of the sawn timber was effective for eliminating timber with lower MOE. Stress-wave velocity and dynamic Young’s modulus of log and timber were significantly correlated with MOE of sawn timber. Correlation coefficients were also significant between MOR of sawn timber and dynamic Young’s modulus or MOE.

Changes in Content of Bioactive Compounds and Antioxidant Activity Induced in Needles of Different Half-Sib Families of Norway Spruce (Picea abies (L.) H. Karst) by Seed Treatment with Cold Plasma.

In order to ensure sufficient food resources for a constantly growing human population, new technologies (e.g., cold plasma technologies) are being developed for increasing the germination and seedling growth without negative effects on the environment. Pinaceae species are considered a natural source of antioxidant compounds and are valued for their pharmaceutical and nutraceutical properties. In this study, the seeds of seven different Norway spruce half-sib families were processed for one or two minutes with cold plasma (CP) using dielectric barrier discharge (DBD) plasma equipment. At the end of the second vegetation season, the total flavonoid content (TFC), DPPH (2,2- diphenyl-1-picryl-hydrazyl-hydrate), and ABTS (2,2’-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid)) antioxidant activity, and the amounts of six organic acids (folic, malic, citric, oxalic, succinic, and ascorbic) were determined in the needles of different half-sib families of Norway spruce seedlings. The results show that the TFC, antioxidant activity, and amounts of organic acids in the seedling needles depended on both the treatment duration and the genetic family. The strongest positive effect on the TFC was determined in the seedlings of the 477, 599, and 541 half-sib families after seed treatment with CP for 1 min (CP1). The TFC in these families increased from 118.06 mg g−1 to 312.6 mg g−1 compared to the control. Moreover, seed treatment with CP1 resulted in the strongest increase in the antioxidant activity of the needles of the 541 half-sib family seedlings; the antioxidant activity, determined by DPPH and ABTS tests, increased by 30 and 23%, respectively, compared to the control. The obtained results indicate that the CP effect on the amount of organic acids in the needles was dependent on the half-sib family. It was determined that treatment with CP1 increased the amount of five organic acids in the needles of the 541 half-sib family seedlings. The presented results show future possibilities for using cold plasma seed treatment in the food and pharmacy industries.

A comparative analysis of Passive Integrated Transponder (PIT) tagging in selective breeding programme of improved rohu (Jayanti) and catla

Passive Integrated Transponder (PIT) tags have been popularly used in identification of individual fish, stock, full-sib and half-sib families, year class and generations in aquaculture selective breeding programs. This study has been conducted on genetically improved Indian Major Carps (IMCs), improved rohu (Jayanti) and improved catla to compare PIT tagging of different size taggable fingerlings with respect to post tagging survival and tag retention. Six groups of improved rohu (Jayanti) and improved catla fingerlings with weight ranging from 10 to 150 g were tagged with PIT tags and mortality was recorded after 24 h. The overall mortality was thus found to be 3 % and 15 % in rohu and catla respectively. In rohu, 3 % mortality was observed after tagging in both small size fish (< 20 g) and large size fish (> 20 g) with no significant difference whereas in catla, mortality in small size fish (< 20 g) was 20 % compared to 14 % in large size fish (> 20 g) (p < 0.05). High correlation of length and weight with tagging space i.e, 0.96 and 0.91 respectively (p < 0.01) was found in rohu while the correlation of length and weight with tagging space was 0.96 and 0.88 respectively (p < 0.01) in catla. In rohu, the correlation of length, weight and tagging space on mortality % was − 0.142, − 0.145 and − 0.173 respectively but not significant (p > 0.05), whereas in catla the correlation of length, weight and tagging space on mortality % was − 0.508, − 0.510, − 0.500 respectively and significant (p < 0.05). Serum cortisol level in control and tagged rohu was 12.98 ± 1.58a ng/ml and 16.09 ± 0.55b ng/ml respectively while the level in control and tagged catla was 12.72 ± 1.56a and 15.97 ± 0.95b ng/ml respectively on the tagging day. There was no significant difference in serum cortisol level in control rohu and control catla and tagged rohu and tagged catla (p > 0.05). This study also revealed more sensitivity of the Indian major carp Labeo catla (Catla) to PIT tagging in comparison to Labeo rohita (rohu) and demonstrates the ideal size for PIT tagging in catla to be 20–30 g.

Experimental insect suppression causes loss of induced, but not constitutive, resistance in Solanumcarolinense.

Spatiotemporal variation in herbivory is a major driver of intraspecific variation in plant defense. Comparatively little is known, however, about how changes in herbivory regime affect the balance of constitutive and induced resistance, which are often considered alternative defensive strategies. Here, we investigated how nearly a decade of insect herbivore suppression affected constitutive and induced resistance in horsenettle (Solanum carolinense), a widespread herbaceous perennial. We allowed replicated horsenettle populations to respond to the presence or absence of herbivores by applying insecticide to all plants in half of 16 field plots. Horsenettle density rapidly increased in response to insecticide treatment, and this effect persisted for at least 4 years after the cessation of herbivore suppression. We subsequently grew half-sibling families from seeds collected during and shortly after insecticide treatment in a common garden and found strong effects of insect suppression on induced resistance. Feeding trials in field mesocosms with false Colorado potato beetles (Leptinotarsa juncta), a common specialist herbivore, revealed that multiyear herbivore suppression drove rapid attenuation of induced resistance: offspring of plants from insect-suppression plots exhibited a near-complete loss of induced resistance to beetles, whereas those from control plots incurred ~70% less damage after experimental induction. Plants from insect-suppression plots also had ~40% greater constitutive resistance compared with those from control plots, although this difference was not statistically significant. We nonetheless detected a strong trade-off between constitutive and induced resistance across families. In contrast, the constitutive expression of trypsin inhibitors (TI), an important chemical defense trait in horsenettle, was reduced by 20% in the offspring of plants from insect-suppression plots relative to those from control plots. However, TIs were induced to an equal extent whether or not insect herbivores had been historically suppressed. Although several defense and performance traits (prickle density, TI concentration, resistance against false Colorado potato beetles and flea beetles, biomass, and seed mass) varied markedly across families, no traits exhibited significant pairwise correlations. Overall, our results indicate that, whereas the divergent responses of multiple defense traits to insect suppression led to comparatively small changes in overall constitutive resistance, they significantly reduced induced resistance against false Colorado potato beetle.

Effects of artificial mating on genomic selection of resistance against Cryptocaryon irritans in large yellow croaker

Genomic selection has been widely used in aquaculture breeding of major aquaculture species. However, the complex environment and mass spawning characteristics make most of the current aquaculture species reproduce the next generation through natural mating, which results in uneven parental contributions, difficulty in tracking high-quality individuals and risk of inbreeding. In this study, we compared the difference in resistance to Cryptocaryon irritans (C. irritans) between artificial insemination pairing and natural mating in large yellow croaker. The reference group consisted of two challenge experimental groups in 2018 and 2020, with 487 and 260 samples, respectively. A total of 381 candidates were selected from the resistant to C. irritans strain (G2) of large yellow croaker constructed in 2019 and genotyped by using 55 K array. The BayesB models and survival time were used to calculate the genomic estimated breeding value (GEBV) of candidates. Finally, a candidate parents population consists of 35 females and 15 males with high estimated breeding value and mature gonads were selected from the resistance against C. irritans strain of large yellow croaker and reproduced two offspring populations due to the characteristics of spawning for two consecutive nights. A natural mating population (T group) was produced on the first spawning night of the parent population, and an artificial mating population contained 19 full-sib and half-sib families (F group) was produced on the second spawning night by the same parents. In addition, a natural mating population (C group) was produced by the unselected strain. A C. irritans infection challenge with duration of 120 h was conducted to compare the performance of disease resistance between the T, F, and C groups. The results showed that the survival rate for T and C groups was 9.85% and 0%, respectively, and the survival rate for F group was ranged from 0% to 63.83%, which 10 families survived significantly longer than the T group. The result showed that the artificially mated can achieved higher phenotypic progress than random mating in the selected breeding of large yellow croaker. This study provides reference for improvement of genomic selection strategy in aquatic species.

Analysis of Transcriptome and Terpene Constituents of Scots Pine Genotypes Inherently Resistant or Susceptible to Heterobasidion annosum.

Root and stem rot caused by Heterobasidion annosum is a severe problem in boreal Scots pine. Dissecting the features of disease resistance is generally an essential step in resistance breeding in plants and forest trees. In this study, we explored inherent resistance factors of Scots pine against H. annosum. A total of 236 families consisting of 85 full-sib (FS), 35 half-sib population mix (HSpm), and 116 half-sib (HS) families of Scots pine seedlings were inoculated with a H. annosum isolate. We sampled needle tissues before inoculation for terpene measurements and RNA sequencing. Based on the lesion area, the extremes of 12 resistant and 12 susceptible families were selected for further analyses. Necrotic lesions resulting from fungal infection were in a weak to moderate relationship with the plant height. Monoterpenes were the principal terpene compounds observed in Scots pine seedlings. Concentrations of 3-carene were significantly higher in pine genotypes inherently resistant compared with susceptible seedlings. By contrast, susceptible genotypes had significantly higher proportions of α-pinene. Gene ontology analysis of differential expressed transcripts (DETs) revealed that response to biotic factors was enriched in resistant seedlings. Functional characterization of individual DETs revealed that higher expression of transcripts involved in response to abiotic stress was common in susceptible genotypes. This observation was supported by the annotation of hub genes in a key module that was significantly correlated with the lesion trait through weighted gene co-expression network analysis (WGCNA) of 16 HS and HSpm samples. These findings contribute to our understanding of constitutive resistance factors of Scots pine against Heterobasidion root and stem rot diseases.

Genomic prediction for canopy height and dry matter yield in alfalfa using family bulks.

Genomic selection (GS) has proven to be an effective method to increase genetic gain rates and accelerate breeding cycles in many crop species. However, its implementation requires large investments to phenotype of the training population and for routine genotyping. Alfalfa (Medicago sativa L.) is one of the major cultivated forage legumes, showing high-quality nutritional value. Alfalfa breeding is usually carried out by phenotypic recurrent selection and is commonly done at the family level. The application of GS in alfalfa could be simplified and less costly by genotyping and phenotyping families in bulks. For this study, an alfalfa reference population composed of 142 full-sib and 35 half-sib families was bulk-genotyped using target enrichment sequencing and phenotyped for dry matter yield (DMY) and canopy height (CH) in Florida, USA. Genotyping of the family bulks with 17,707 targeted probes resulted in 114,945 single-nucleotide polymorphisms. The markers revealed a population structure that matched the mating design, and the linkage disequilibrium slowly decayed in this breeding population. After exploring multiple prediction scenarios, a strategy was proposed including data from multiple harvests and accounting for the G×E in the training population, which led to a higher predictive ability of up to 38 and 24% for DMY and CH, respectively. Although this study focused on the implementation of GS in alfalfa families, the bulk methodology and the prediction schemes used herein could guide future studies in alfalfa and other crops bred in bulks.

SNP Detection in Pinus pinaster Transcriptome and Association with Resistance to Pinewood Nematode

Pinewood nematode (PWN, Bursaphelenchus xylophilus) is the causal agent of pine wilt disease (PWD), which severely affects Pinus pinaster stands in southwestern Europe. Despite the high susceptibility of P. pinaster, individuals of selected half-sib families have shown genetic variability in survival after PWN inoculation, indicating that breeding for resistance can be a valuable strategy to control PWD. In this work, RNA-seq data from susceptible and resistant plants inoculated with PWN were used for SNP discovery and analysis. A total of 186,506 SNPs were identified, of which 31 were highly differentiated between resistant and susceptible plants, including SNPs in genes involved in cell wall lignification, a process previously linked to PWN resistance. Fifteen of these SNPs were selected for validation through Sanger sequencing and 14 were validated. To evaluate SNP-phenotype associations, 40 half-sib plants were genotyped for six validated SNPs. Associations with phenotype after PWN inoculation were found for two SNPs in two different genes (MEE12 and PCMP-E91), as well as two haplotypes of HIPP41, although significance was not maintained following Bonferroni correction. SNPs here detected may be useful for the development of molecular markers for PWD resistance and should be further investigated in future association studies.