Half-sib Offspring Research Articles

Unlocking Cassava Brown Streak Disease Resistance in Cassava: Insights from Genetic Variability and Combining Ability

Cassava brown streak disease (CBSD) threatens cassava production in sub-Saharan Africa despite the availability of resistant varieties. Extreme environmental factors weaken plant defenses, reducing CBSD resistance. This study examined CBSD inheritance in cassava populations, assessed genetic variability, and identified superior sources of resistance using F1, S1, and half-sib offspring populations derived from resistant sources. The offspring underwent field evaluation at two distinct sites from 2019 to 2021, and the symptom-free genotypes were analyzed using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Resistance to CBSD was categorized as most resistant, resistant, most tolerant, or tolerant based on symptoms and virus titers. The findings indicated that the resistance to CBSD is highly influenced by genotypes, F1/S1 types, and environmental conditions. An analysis of combining abilities revealed significant general combining abilities (GCAs) for CBSD, cassava mosaic disease (CMD), and traits associated with yield. The heritability estimates for resistance to CBSD varied between 43.4% and 63.2% for foliar symptoms and 14.6% and 57.9% for root necrosis across locations. The inheritance pattern involved a combination of additive and recessive genes with selfed (S1) populations displaying stronger and more effective resistance to the disease. The cassava brown streak virus (CBSV) was highly prevalent, and the Ugandan cassava brown streak virus (UCBSV) was not prevalent. Four genotypes were highly resistant to CBSD and could be key sources of resistance to this disease.

VARIABILITY OF LEAVES PARAMETERS IN ORIENTAL PLANE TREE (PLATANUS ORIENTALIS L.)

This paper presents the results of leaves parameters measuring of Oriental plane tree (Platanus orientalis L.), a rare tree species of Bulgarian flora naturally occurring only along the river streams in the southern part of the country. Based on morphometric parameters, the variability of the leaves of the oriental plane tree in 8 natural habitats (Asenovgrad, Topolovo, Sandanski, Melnik, Petrich, Slavyanka, Gotse Delchev and Ivaylovgrad) of the species in Bulgaria has been investigated. A higher degree of variability was observed between half-sib offspring than between populations. Eight parameters of the leaves were measured, in most cases the population from Asenovgrad is superior to the other origins. The results show that the most differentiated features are the length of the leafstalk (LD) and the length of the middle lobe (L). The size and shape of the leaves are relatively homogeneous and this makes difficult to determine individual origins only by leaves.

A temporal assessment of family composition and genetic diversity in a commercial cohort of Dusky Kob, Argyrosomus japonicus, across the production cycle

The reproductive modes and life history of aquaculture species, such as dusky kob (Argyrosomus japonicus), characterised by high fecundity, mass larval mortality and skewed broodstock spawning success, poses a challenge for the implementation of selective breeding programmes. This often results in inbreeding and the loss of genetic diversity and reduced overall population productivity. These effects might be further exacerbated by standard aquaculture production practices, such as size grading and culling, but this remains under-investigated. In the present study, 14 microsatellite markers were used to monitor changes in genetic diversity and family compositions throughout the production cycle of F1 dusky kob (weaning to marketable size). Overall, the F1 animals experienced a substantial reduction in allelic content and presented statistically significant differentiation from the wild, with a global FST of 0.03 (P < 0.01). Parentage analyses indicated an effective broodstock population size of only seven (out of 12) individuals, with only five full-sib families (from a potential of 16) and three half-sib offspring groups. Two families each had a starting contribution, at weaning, of less than 5%, though neither was eliminated following removal of the smallest animals by grading and culling. Culling, at the final stage, however, did contribute to a significant increase in genetic relatedness in the oldest (i.e. market-sized) group analysed and a single family represented 88% of the resulting stock, suggesting that these individuals were on average faster growing than others. The obtained results demonstrate that culling practices do have the potential to create bias in the representation of families, further complicating the selection of unrelated broodstock candidates in selective breeding programmes.

Variance, Genetic Control, and Spatial Phenotypic Plasticity of Morphological and Phenological Traits in Prunus spinosa and Its Large Fruited Forms (P. x fruticans).

Prunus spinosa is a highly esteemed shrub in forest and landscape plantings. Shrubs with larger organs occur often and are considered either as large fruited forms of P. spinosa or as P. x fruticans, involving a hybridization process with the ancient cultivated P. insititia (crop-to-wild gene flow). As climate change may augment hybridization processes in the future, a hybrid origin is important to detect. In addition, studying crop-to-wild gene flow can give insights in putative consequences for the wild populations. We studied the P. spinosa–P. x fruticans group, focusing on morphology and phenology in three experimental plantations. Two plantings harbored cuttings of P. spinosa (clone plantations). A third plantation comprised of a half-sib offspring from a population with both P. spinosa and P. x fruticans (family plantation). Several results point to a hybridization process as the origin of P. x fruticans. The clone plantation revealed endocarp traits to be more genetically controlled than fruit size, while this was the opposite in the family plantation, suggesting the control of fruit size being derived from the putative P. insititia parent. Bud burst, flower opening, and leaf fall were genetically controlled in the clone plantation, whereas in the family plantation intrafamily variability was remarkably large for the bud burst and leaf fall, but not for the flower opening. This suggests there is a reduced genetic control for the first two phenophases, possibly caused by historic hybridization events. Pubescence on the long shoot leaves in the family plantation deviated from the short shoot leaves on the same plants and from long and short shoot leaves in the clone plantation, suggesting again a P. insititia origin. Finally, we quantified spatial phenotypic plasticity, indicating how P. spinosa may react in a changing environment. In contrast to the bud burst and leaf fall, flower opening did not demonstrate plasticity. The fruit size was diminished at the growth site with the shortest growing season while interestingly, the leaf width was enlarged. Leaf size traits appeared more plastic on the long shoots compared to the short shoots, although partitioning of variance did not display a lesser genetic control.

Heritability and phenotypic variation of double seeds in almond (Prunus dulcis)

In almond, the presence of double seeded nuts significantly reduces their commercial value. For this reason, in breeding programs of this species, seedlings producing double seeds are usually eliminated. In order to avoid this trait in the offspring and increase the efficiency of the breeding programs it is important to know its genetic control. In this work, heritability of double seeds was estimated by midparent–offspring regression (narrow sense, h2) and by variance components analysis (broad sense, H2) for 3 years, in a population with a combination of full-sib and half-sib offspring coming from eight crosses designed for this objective. Heritability was high by both methods every year, and the values calculated by variance components were higher than those estimated by regression. The average ratio h2/H2 0.69 implies some influence of a non-additive effect for this trait, such as dominance and environmental effect. In this case, the influence of the temperatures preceding blooming on the percentage of double seeds can be inferred from our results, with lower temperatures increasing the percentage of double seeds. In the crosses between parents with high percentage of double seeds a normal (Gaussian) phenotypic distribution was observed. For crosses between one parent without double seeds and parents with high-medium percentage of double seeds a right-skew distribution (L-shaped) was observed, and certain transgressive segregation was observed in the descendants. This transgressive segregation was confirmed when both parents presented null percentage of double seeds. The results confirmed the complex architecture of this trait transmitted quantitatively, where additive, non-additive and genotype-by-environment interaction effects play an important role.

Incest versus abstinence: reproductive trade‐offs between mate limitation and progeny fitness in a self‐incompatible invasive plant

Plant mating systems represent an evolutionary and ecological trade-off between reproductive assurance through selfing and maximizing progeny fitness through outbreeding. However, many plants with sporophytic self-incompatibility systems exhibit dominance interactions at the S-locus that allow biparental inbreeding, thereby facilitating mating between individuals that share alleles at the S-locus. We investigated this trade-off by estimating mate availability and biparental inbreeding depression in wild radish from five different populations across Australia. We found dominance interactions among S-alleles increased mate availability relative to estimates based on individuals that did not share S-alleles. Twelve of the sixteen fitness variables were significantly reduced by inbreeding. For all the three life-history phases evaluated, self-fertilized offspring suffered a greater than 50% reduction in fitness, while full-sib and half-sib offspring suffered a less than 50% reduction in fitness. Theory indicates that fitness costs greater than 50% can result in an evolutionary trajectory toward a stable state of self-incompatibility (SI). This study suggests that dominance interactions at the S-locus provide a possible third stable state between SI and SC where biparental inbreeding increases mate availability with relatively minor fitness costs. This strategy allows weeds to establish in new environments while maintaining a functional SI system.

Estimation of genetic variance for macro- and micro-environmental sensitivity using double hierarchical generalized linear models.

BackgroundGenetic variation for environmental sensitivity indicates that animals are genetically different in their response to environmental factors. Environmental factors are either identifiable (e.g. temperature) and called macro-environmental or unknown and called micro-environmental. The objectives of this study were to develop a statistical method to estimate genetic parameters for macro- and micro-environmental sensitivities simultaneously, to investigate bias and precision of resulting estimates of genetic parameters and to develop and evaluate use of Akaike’s information criterion using h-likelihood to select the best fitting model.MethodsWe assumed that genetic variation in macro- and micro-environmental sensitivities is expressed as genetic variance in the slope of a linear reaction norm and environmental variance, respectively. A reaction norm model to estimate genetic variance for macro-environmental sensitivity was combined with a structural model for residual variance to estimate genetic variance for micro-environmental sensitivity using a double hierarchical generalized linear model in ASReml. Akaike’s information criterion was constructed as model selection criterion using approximated h-likelihood. Populations of sires with large half-sib offspring groups were simulated to investigate bias and precision of estimated genetic parameters.ResultsDesigns with 100 sires, each with at least 100 offspring, are required to have standard deviations of estimated variances lower than 50% of the true value. When the number of offspring increased, standard deviations of estimates across replicates decreased substantially, especially for genetic variances of macro- and micro-environmental sensitivities. Standard deviations of estimated genetic correlations across replicates were quite large (between 0.1 and 0.4), especially when sires had few offspring. Practically, no bias was observed for estimates of any of the parameters. Using Akaike’s information criterion the true genetic model was selected as the best statistical model in at least 90% of 100 replicates when the number of offspring per sire was 100. Application of the model to lactation milk yield in dairy cattle showed that genetic variance for micro- and macro-environmental sensitivities existed.ConclusionThe algorithm and model selection criterion presented here can contribute to better understand genetic control of macro- and micro-environmental sensitivities. Designs or datasets should have at least 100 sires each with 100 offspring.

Heritability of Morphological Traits in Apple Early-ripening Full-sib and Half-sib Offspring and Its Potential Use for Assisted Selection

To select the superior parents for the breeding program we oriented to produce new early-ripening cultivars, we evaluated more than 60 productive and vegetative characters in 108 native and imported cultivars grown in national collection for commercial apples located in Karaj, Iran, using an apple descriptor. The germination percentage of 100,000 hybrid seeds was 7% in the first year. In the second year, only 3000 from 7000 seedlings had to pass the final screening. Use of morphological markers as an early selection technique showed high efficiency in the apple breeding program. This study was conducted to determine heritability of certain morphological traits potentially used for selection of fruit early-ripening progenies in apple (Malus ×domestica Borkh.). Morphological traits in 3- and 4-year-old seedlings from 28 half-sib and 16 full-sib families were studied in 2007 and 2008, respectively. Parent–progeny correlations were analyzed using true-to-type progenies and their relative parents, all in the juvenile phase. Significant variations were observed between parental cultivars and half-sib and full-sib progenies for most of the studied traits. Positive correlations were found between seedling height and other morphological characters. A highly significant correlation (r = 0.98) was observed between branch distance along seedling stem and number of branches. The results showed that the heritability varied among the traits, ranging from moderate to high values. A high level of heritability was found in leaf chlorophyll concentration (LCC) and seedling heights in both half-sib and full-sib families. Heritability of half-sib progenies derived from the early-ripening parents was higher than the late-ripening parents. The relatively high heritability estimates for morphological traits, particularly in early-ripening cross combinations, suggested narrow-sense heritability as a criterion for early screening. The progenies of early cultivars exhibited the maximum and minimum heritability for seedling height (0.91) and leaf length (0.56), respectively. Oppositely, in the late-ripening progenies, the maximum and minimum heritability were found in LW and TD traits (0.79 and 0.42), respectively.

Relationship between autumn cold hardiness and field performance in northern Pinus sylvestris

Results from 3 artificial freezing tests (one-year-old seedlings) and 15 field trials (9- to 21-year old trees) of half-sib offspring from first generation Scots pine (Pinus sylvestris L.) plus-trees were used to estimate the amount of additive genetic variance for autumn cold hardiness and traits assessed in the field, and the genetic correlations between them. Cold hardiness of individual seedlings was scored visually, based on the discoloration of their needles after freezing in a climate chamber. The field traits analyzed were tree vitality, tree height, spike knot frequency, branch diameter, branch angle, stem straightness, and susceptibility to infection by the pathogenic fungi Phacidium infestans L., Gremmeniella abietina (Lagerb.) Morelet, Melampsora pinitorqua (Braun) Rostr. and Lophodermella sulcigena (Rostr.) Höhn. Narrow sense individual heritabilities varied between 0.30 and 0.54 for autumn cold hardiness, 0 and 0.18 for tree vitality, 0.07 and 0.41 for tree height, and 0.01 and 0.26 for the remaining traits. Based on the results of the artificial freeze tests, our estimates of additive genetic correlations indicate that while early selection for cold hardiness can improve seedling survival rates in the field, it may also reduce growth in mild environments. It also has minor effects on quality traits and attack by common fungal diseases. The results indicate that artificial freeze testing is an appropriate method for identifying suitable clones for establishing seed orchards to supply stock for the reforestation of regions with harsh environments.

Inferring unknown genotypes of sires at codominant deoxyribonucleic acid markers in half-sib families1

Deoxyribonucleic acid from sires is usually not available from experiments aimed at QTL mapping for traits of the dam in cow-calf operations and free range sheep populations. In this study, methods to reconstruct sire genotypes using genotype information from large half-sib progeny were developed. The methods are based on 1) all offspring genotypes are compatible with more than 1 genotype for the sire, but 1 of the genotypes is more likely than the others when comparing the proportion of the different genotypes among offspring with its expected values assuming Mendelian inheritance, or 2) all offspring genotypes are compatible with just 1 possible genotype for the sire in the pedigree. A Monte Carlo simulation experiment was carried out to test the methods with 1 million replicates. A 99.7% correct sire genotype reconstruction was obtained with 30 offspring and a DNA marker with 3 or more alleles segregating at similar frequencies. Methods to test for incorrect paternity in half-sib offspring without DNA from the sire were also developed. A maximum likelihood method was developed to test for departure of Mendelian segregation due to a contaminating sire whose offspring are fully compatible with the genotype of the pedigree sire. A large number of offspring was needed to detect offspring from a contaminating sire (1,000 progeny for a power of 0.99 and proportion of true paternity of the pedigree of 0.80). Multi-marker methods were also developed for detection of paternity misidentification. Probabilities of detection of wrong paternity for a contaminating sire not sharing any alleles with the sire in the pedigree were 0.95 and 0.99 when using 5 and 10 markers in 30 half-sib offspring, respectively. The methods to infer the sire genotypes were tested with 49 progeny of a Merino ram whose genotype was inferred for 7 microsatellites. Methods to infer genotype of the sire are feasible, but QTL mapping experiments without DNA from the sires are more costly due to the need of genotyping markers in progeny for which the sire in the pedigree is homozygous.

A directed search around caprine candidate loci provided evidence for microsatellites linkage to growth and cashmere yield in Rayini goats

Four genomic regions located on goat chromosomes 1, 2, 5 and 13 previously reported as significant DNA regions harboring quantitative trait loci (QTL) for growth and fleece traits in goat were considered as candidate genomic regions. The objective of conducting this study was to determine whether there is evidence for association of growth traits and cashmere yield in native Iranian Rayini goats with markers flanking these candidate regions. One hundred and twenty kids from 6 Rayini bucks (20 half-sib offspring per buck) were used in the present study. The six bucks and their offspring were genotyped for eight microsatellite markers flanking the candidate intervals. Body weights recorded on the kids were birth weight (BW0), weaning weight (BW3) and weight at 6 months of age (BW6). Average daily gains from birth to weaning and weaning to 6 months of age were computed based on the values obtained for BW0, BW3 and BW6. Cashmere yield was also recorded for the kids at the first, second and third year of age. QTL analysis in the candidate intervals was conducted using the least squared regression interval mapping approach. Linkage analysis indicated significant QTL for growth traits on goat chromosomes 1, 2 and 5 (chromosome-wide significance of P < 0.01). Three of the candidate regions located on chromosomes 2, 5 and 13 were linked to cashmere yield. QTL effect ranged from 0.8 to 4.3 in units of residual standard deviation for different traits and families.

Effects of origin, experiences early in life, and genetics on bitterweed consumption by sheep

Bitterweed is one of the most detrimental poisonous plants to sheep production in west central Texas. Sheep typically avoid the plant unless alternative forage is limited. When consumption does occur, some flocks and individuals are able to consume bitterweed and avoid toxicosis. Our objective was to determine the importance of site of origination (long-term exposure), experiences early in life (short-term exposure), and sire selection on the ability to avoid bitterweed toxicity. In Trial 1, we compared bitterweed intake of 15 ewes originating from bitterweed-infested and 15 ewes from bitterweed-free rangelands. Bitterweed intake of their half-sib offspring was compared in the subsequent year. Ewes from bitterweed-infested rangelands ate more ( P<0.05) bitterweed, but lambs born to ewes from bitterweed-free rangelands consumed more ( P<0.05) bitterweed. In Trial 2, we compared intake of 40 lambs from two separate ewe flocks (20 from each flock). One flock of ewes originated from bitterweed-infested rangelands, the other from bitterweed-free rangelands. Each flock was divided in half so that irrespective of origin of the ewes, lambs from both flocks would be born and reared (birth to weaning) in each habitat. Lambs from flocks originating from bitterweed-free rangelands consumed more bitterweed than lambs from bitterweed-infested rangelands, regardless of site of rearing. During Trials 2 and 3, we also assessed the influence of sire on bitterweed intake. Offspring from three sires in Trial 2 consumed different ( P<0.05) amounts of bitterweed, but sires were confounded with origin. In Trial 3, offspring from five unrelated sires consumed similar amounts of bitterweed. Thus, the ability to consume bitterweed does not appear to be strongly influenced by the sire’s genetic characteristics. Likewise, experience with bitterweed early in life does not appear to lead to greater consumption later in life. Thus, manipulating feeding behavior does not appear to be a viable management option at this time for reducing the likelihood of bitterweed toxicosis.

Biased estimation of the recombination fraction using half-sib families and informative offspring.

A maximum-likelihood method to estimate the recombination fraction and its sampling variance using informative and noninformative half-sib offspring is derived. Estimates of the recombination fraction are biased up to 20 cM when noninformative offspring are discarded. In certain scenarios, the sampling variance can be increased or reduced up to fivefold due to the bias in estimating the recombination fraction and the LOD score can be reduced up to 5 units when discarding noninformative offspring. Comparison of the estimates of recombination fraction, map distance, and LOD score when constructing a genetic map with 251 two-point linkage analyses and six families of Norwegian cattle was carried out to evaluate the implications of discarding noninformative offspring in practical situations. The average discrepancies in absolute value (average difference when using and neglecting noninformative offspring) were 0.0146, 1.64 cM, and 2.61 for the recombination fraction, map distance, and the LOD score, respectively. A method for simultaneous estimation of allele frequencies in the dam population and a transmission disequilibrium parameter is proposed. This method might account for the bias in estimating allele frequencies in the dam population when the half-sib offspring is selected for production traits.

Marker controlled inheritance of the polled locus in Simmental cattle

Abstract. The inheritance of the polled phenotype in Simmental cattle was tested for linkage with alleles of four microsatellite markers on the proximal region of BTA1. For the study half-sib offspring of three sires were selected which are known to be heterozygous for the polled condition. The analysis of 57 animals (42 polled and 15 horned) revealed complete linkage between the polled locus and the markers BM6438 and SODlMicro2. The reliability of the prediction of the hörn Status of the offspring for marker assisted selection was estimated from its marker genotype in comparison to the patemal haplotype phases responsible for polledness, and from the allele frequencies of the favoured marker alleles in the random population.

Report of the International Equine Gene Mapping Workshop: male linkage map.

The goal of the First International Equine Gene Mapping Workshop, held in 1995, was the construction of a low density, male linkage map for the horse. For this purpose, the International Horse Reference Family Panel (IHRFP) was established, consisting of 12 paternal half-sib families with 448 half-sib offspring provided by 10 laboratories. Blood samples were collected and DNA extracted in each laboratory and sent to the Lexington laboratory (KY, USA) for dispatch in aliquots to 14 typing laboratories. In total, 161 markers (144 microsatellites, seven blood groups and 10 proteins) were tested for all families for which the sire was heterozygous. Genealogies and typing data were sent for analysis to the INRA laboratory (Jouy-en-Josas, France) according to a specific format and entered into a database with input verification and output processes. Linkage analysis was performed with the CRIMAP program. Significant linkage was detected for 124 loci, of which 95 were unambiguously ordered using a multipoint analysis with an average spacing of 14.2 CM. These loci were distributed among 29 linkage groups. A more comprehensive analysis including synteny group data and FISH data suggested that 26 autosomes out of 31 are covered. The complete map spans 936 CM.

Power of two and three-generation QTL mapping experiments in an outbred population containing full-sib or half-sib families

QTL mapping experiments involve many animals to be genotyped and performance tested. Consequently, experimental designs need to be optimized to minimize the costs of data collection and genotyping. The present study has analyzed the power and efficiency of experiments with two or three-generation family structures containing full-sib families, half-sib families, or both. The focus was on data from one outbred population because the main interest is to locate genes that can be used for within-line selection. For a two generation experiment more animals had to be typed for marker loci to obtain a certain power than for a three generation experiment. Fewer trait values, however, had to be obtained for a two-generation experiment than for a three-generation experiment. A two or three-generation family structure with full-sib offspring was more efficient than a two or three-generation family structure with half-sib offspring. A family structure with full-sib grand-offspring, however, was less efficient than a family structure with half-sib grand-offspring. For the most efficient family structure each pair of parents had full-sib offspring that were genotyped for the marker. For the most-efficient family structure each full-sib offspring had half-sib grand-offspring for which trait values were obtained. For equal power with a heritability of 0.1 and 100 grand-offspring per full-sib offspring, 30-times less marker typings were required for this most efficient family structure than for a two-generation half-sib structure in which marker genotypes and trait values were obtained for half-sib offspring. The effect of heritability and the type of analysis (single marker or interval analysis) on the efficiency of a family structure is described. The results of this study should help to design QTL mapping experiments in an outbred population.

Untersuchungen zur Morphologie und Nadelanatomie der F1-Generation einer Schlangenfichte

Half sib offspring of a snake-spruce was investigated morphologically and compared with the normal form and the snake-spruce mother. In trees with increasing “snake” character the diameter of the stem, the branching and the height of the whole tree and the dry matter content of the needles increases. The needles of the snake-form are longer and broader. These larger needles result from an increase of cell size rather than from an increase of cell number. Snake forms are more xeromorphic: their cuticles are thicker, the stomatal chambers are deeper, and the number of sclereids is higher. The needles of snake-spruces have characters of light leaves.

HERITABILITY AND GENETIC CORRELATION OF SOLUBLE SOLIDS, BULB SIZE AND SHAPE IN WHITE SWEET SPANISH ONION

Heritability of size, shape and soluble solids content of bulbs in a White Sweet Spanish onion cultivar (Allium cepa L.) was estimated in two ways: (1) by calculating regressions of half-sib offspring on female parent, and (2) by calculating half-sib family intra-class correlations. Heritabilities of bulb weight and diameter were low (0 and 28%; 0 and 27%); bulb height, intermediate (45 and 48%); shape index and solids, high (89 and 62%; 79 and 82%). Phenotypic correlations among five variables were separated into additive genetic and environmental correlations. The data contain negative genetic correlations between solids and bulb size; if confirmed, such a relationship would be of concern to plant breeders when selecting onions for higher solids content.