PSI-B-21 Alternative SNP weighting for multi-step and single-step genomic BLUP in the presence of causative variants

This study aimed to evaluate the accuracy of genomic prediction with simulated data, using SNP markers, causal quantitative trait nucleotide (QTN), and the combination of both. The methods used were the best linear unbiased prediction (GBLUP) and single-step GBLUP (ssGBLUP), with alternative SNP weights. Data were simulated using the package AlphasimR. Trait heritability of 0.3 was assumed, and genetic variance was fully accounted for by 100 or 1000 QTNs. A population with an effective size of 200 was selected, and 20 generations were simulated. The genomic information mimicked the 29 bovine chromosomes and included 50k SNP markers evenly distributed across the genome. Approximately 16800 genotypes were available from selected sires and dams in generations 16–19, and 2000 animals in generation 20. Phenotypes for young animals were not included in the analysis, as they were used in the validation. For GBLUP, three pseudo-phenotypes were considered: the raw phenotype, the true breeding value, and the true breeding value with noise added. The genomic relationship matrix was weighted using quadratic weights, calculated based on the SNP variance, and non-linear A, following different equation parameters. The scenario with exclusively causal variants presented accuracies close to 1 for 100 QTL, and slightly lower in the 1000 QTL. For the SNP + QTN scenario, quadratic weights promoted higher accuracy gains than the SNPs alone, especially in the 100 QTN trait. Accuracies converged at higher values for both quadratic and non-linear A weights in the 100 QTN scenario. For the 1000 QTN trait, quadratic weights diverged and reduced accuracy, while non-linear A maintained accuracy at their peaks, depending on the equation parameters. Parameters of non-linear A for highest accuracy were different in each scenario and type of analysis. Proportionally, gains in accuracy were more prominent with GBLUP than with ssGBLUP.

Prey Capture in Anthocyanin-free Sarracenia leucophylla (Sarraceniaceae) Is Associated with Leaf Size, But Not Red Pigmentation

Anthocyanin pigmentation is a significant horticultural feature in plants and can be a crucial mediator of plant–insect interactions. In carnivorous plants, the modified leaves that capture prey can be visually striking and are traditionally considered prey attractants. Nevertheless, the question of whether bold color and venation patterns function as lures for insect prey remains ambiguous, and appears to vary across taxa. Furthermore, vegetative pigments can have alternate functions as protectants against thermal and oxidative damage. Our dual-year study compares the wild-type pitcher phenotype with a true-breeding anthocyanin-free mutant of the white-topped pitcher plant (Sarracenia leucophylla Raf.). We bred full-sibling crosses of S. leucophylla carrying either the wild-type anthocyanin gene or the anthocyanin-free variant. In both experimental years, growth points were established in outdoor plots and pitchers were allowed to capture prey before harvest at the end of each growing season. Dry weight of prey biomass was measured from pitchers of both pigment morphs, along with nectary counts, pitcher size, and internal temperature. The presence of anthocyanins in trapping leaves did not affect the biomass of insects captured. Nor did wild-type or anthocyanin-free pitcher morphs differ in size, temperature, or nectary counts. Instead, pitcher height, and, nominally, mouth diameter were better predictors of prey biomass. Despite striking visual differences in pitcher color, wild-type and anthocyanin-free plants did not catch significantly different quantities of prey. Our study provides empirical data that anthocyanin pigmentation in S. leucophylla does not affect the capture of prey biomass, and supports a growing body of literature showing that pigmentation traits serve in multiple contexts.

Restricted Selection Index to Relieve the Negative Repercussion in Reproductive Performance of Holstein Cows

The aim of this investigation was to develop restricted selection index aiming to improve 305-day yields of milk (MY), fat (FY) and protein (PY), while keeping the deterioration in days open (DO), calving interval (CI) and number of services per conception (NSPC) at minimum levels in Holstein cows. The data represent 3682 records of 1122 cows, daughters of 95 sires and 712 dams. The data were analyzed by multi-trait animal model with repeated measures. Eight selection indexes (five unrestricted and three restricted) were derived using MY, FY, PY, CI, DO and NSPC in various combinations as sources of information in the indexes. However, the true breeding value included MY, FY and PY. The highest accuracy of selection (0.60) resulted from selection based on the full index. Milk yield and SPC appeared to be the most valuable traits in the full index. Combining the two traits into one index (the best reduced index) gave 0.57 accuracy of selection. The index based on MY alone (the most accurate single trait index) gave 0.53 accuracy. It seems possible to reduce the expected genetic deterioration in the reproductive traits by restricting the full index to result in zero genetic change in NSPC (rTI=0.48). This restriction will allow the breeder to mitigate the deterioration in DO and CI by 12 and 16 days respectively, by sacrificing with part of the expected genetic improvement in productive traits (29, 40 and 48% in MY, FY and PY, respectively).

Temperature-Inducible Precision Guided Sterile Insect Technique

Releases of sterile males are the gold standard for many insect population control programs, and precise sex sorting to remove females prior to male releases is essential to the success of these operations. To advance traditional methods for scaling the generation of sterile males, we previously described a CRISPR-mediated precision-guided sterile insect technique (pgSIT), in which Cas9 and gRNA strains are genetically crossed to generate sterile males for release. While effective at generating F1 sterile males, pgSIT requires a genetic cross between the two parental strains which requires maintenance and sexing of two strains in a factory. Therefore, to further advance pgSIT by removing this crossing step, here we describe a next-generation Temperature-Inducible pgSIT (TI-pgSIT) technology and demonstrate its proof-of-concept in Drosophila melanogaster. Importantly, we were able to develop a true-breeding strain for TI-pgSIT that eliminates the requirement for sex sorting, a feature that may help further automate production at scale.

Phenotype study of multifoliolate leaf formation inTrifolium alexandrinumL.

BackgroundThe genusTrifoliumis characterized by typical trifoliolate leaves. Alterations in leaf formats from trifoliolate to multifoliolate, i.e., individual plants bearing trifoliolate, quadrifoliolate, pentafoliolate or more leaflets, were previously reported among many species of the genus. The study is an attempt to develop pure pentafoliolate plants ofT. alexandrinumand to understand its genetic control.MethodsThe experimental material consisted of two populations ofT. alexandrinumwith multifoliolate leaf expression, i.e.,interspecific hybrid progenies ofT. alexandrinumwithT. apertum, andT. alexandrinumgenotype Penta-1. Penetrance of the multifoliolate trait was observed among multifoliolate and trifoliolate plant progenies. In vitro culture and regeneration of plantlets from the axillary buds from different plant sources was also attempted.ResultsThe inheritance among a large number of plant progenies together with in vitro micro-propagation results did not establish a definite pattern. The multifoliolate leaf formation was of chimeric nature, i.e., more than one leaf format appearing on individual branches. Reversal to normal trifoliolate from multifoliolate was also quite common. Penetrance and expression of multifoliolate leaf formation was higher among the plants raised from multifoliolate plants. Multifoliolate and pure pentafoliolate plants were observed in the progenies of pure trifoliolate plants and vice-versa. There was an apparent increase in the pentafoliolate leaf formation frequency over the years due to targeted selection. A few progenies of the complete pentafoliolate plants in the first year were true breeding in the second year. Frequency of plantlets with multifoliolate leaf formation was also higher in in vitro axillary bud multiplication when the explant bud was excised from the multifoliolate leaf node.ConclusionNumber of leaflets being a discrete variable, occurrence of multifoliolate leaves on individual branches, reversal of leaf formats on branches and developing true breeding pentafoliolates were the factors leading to a hypothesis beyond normal Mendelian inheritance. Transposable elements (TEs) involved in leaf development in combination with epigenetics were probably responsible for alterations in the expression of leaflet number. Putative TE’s movement owing to chromosomal rearrangements possibly resulted in homozygous pentafoliolate trait with evolutionary significance. The hypothesis provides a new insight into understanding the genetic control of this trait inT. alexandrinumand may also be useful in otherTrifoliumspecies where such observations are reported.

Selective genotyping and phenotypic data inclusion strategies of crossbred progeny for combined crossbred and purebred selection in swine breeding

Inclusion of crossbred (CB) data into traditionally purebred (PB) genetic evaluations has been shown to increase the response in CB performance. Currently it is unrealistic to collect data on all CB animals in swine production systems, thus, a subset of CB animals must be selected to contribute genomic/phenotypic information. The aim of this study was to evaluate selective genotyping strategies in a simulated 3-way swine crossbreeding scheme. The swine crossbreeding scheme was simulated and produced 3-way CB animals for 6 generations with three distinct purebred breeds each with 25 and 175 mating males and females, respectively. F1 crosses (400 mating females) produced 4,000 terminal CB progeny which were subjected to selective genotyping. The genome consisted of 18 chromosomes with 1,800 QTL and 72k SNP markers. Selection was performed using estimated breeding values (EBV) for CB performance. It was assumed that both PB and CB performance was moderately heritable (h2=0.4). Several scenarios altering the genetic correlation between PB and CB performance (rpc=0.1, 0.3, 0.5, 0.7 or 0.9) were considered. CB animals were chosen based on phenotypes to select 200, 400 or 800 CB animals to genotype per generation. Selection strategies included: 1) Random: random selection, 2) Top: highest phenotype, 3) Bottom: lowest phenotype, 4) Extreme: half highest and half lowest phenotypes, and 5) Middle: average phenotype. Each selective genotyping strategy, except for Random, was considered by selecting animals in half-sib (HS) or full-sib (FS) families. The number of PB animals with genotypes and phenotypes each generation was fixed at 1680. Each unique genotyping strategy and rpc scenario was replicated 10 times. Selection of CB animals based on the Extreme strategy resulted in the highest (P<0.05) rates of genetic gain in CB performance (ΔG) when rpc<0.9. For highly correlated traits (rpc=0.9) selective genotyping did not impact (P>0.05) ΔG. No differences (P>0.05) were observed in ΔG between Top, Bottom or Middle when rpc>0.1. Higher correlations between true breeding values (TBV) and EBV were observed using Extreme when rpc<0.9. In general, family sampling method did not impact ΔG or the correlation between TBV and EBV. Overall, the Extreme genotyping strategy produced the greatest genetic gain and the highest correlations between TBV and EBV, suggesting that two tailed sampling of CB animals is the most informative when CB performance is the selection goal.

Genetic resources in Finnish landrace rye (Secale cereale) and experimental evolving of its spring-habit from winter rye

Rye was the most important grain crop in Finland towards the end of the 19th century. Rye was largely grown in burned lands, kaski (slash-and-burn) and kytö, in the past. In the primary form of kytö, shoveled topsoil was heated on fires slowly combusting extraneous wood, brushwood or reed, or in the secondary form, a dry upper layer of organic topsoil of field was burned in a prescribed frontal mode in situ. The kytö selected against the brittle spike type, largely eliminating the weedy seed banks in the soil. Likewise, seed handling, especially the common cleaning with a pohdin -device further eliminated partially brittle spike types and selected against weedy rye. Rye was a cash-crop for the peasants in the past and was mainly attempted to be exported as seed. The commonly used smoky riihi-drying sanitized and conserved grains, which retained germinabilty, and in part increased demand for seed abroad. The grains produced on burned lands were fortified with minerals, including the minor elements, and good winter-hardiness occurred in the Finnish rye. The immigrant Finns were probably the first since 1638 to grow rye from seeds brought along with them to New Sweden in North America, where de-domesticated or feral rye became a weed problem in the 1950s. Some genetically variable landraces could be sown during different times of the year, thanks to segregate plants adapted to different sowing-times. Sowing of a winter rye landrace in May, the season of spring grain sowing, enabled selection of spring-habit mutants or segregants, which could be used to establish a true-breeding spring stock of rye shown experimentally. In the past, mid-summer sowing could occur with co-cultivation, e.g. with the traditional slash-and-burn turnip as the first season crop, or the autumn seedling of rye could be used as pasture. The Finnish rye populations frequently had cytoplasmic male sterility (CMS) and nuclear restorer genes of anther fertility effective in the CMS. A non-leaky CMS and a leaky CMS (with male fertility in the late stems) are shown. Homozygosity obtained through forced self-pollination in a Finnish rye revealed unnoticed genes, such as dwarfs. A local rye population originating from Putkosjärvi area (64° 27’ N), in Ristijärvi Municipality, evidently devoid of the frequently contaminating weed, rye brome (Bromus secalinus), is thought to present an uncontaminated, ancient Finnish rye. The rye brome has contaminated growth in Finland at least since the Iron Age. Morphological variants, like brown spike or glume color and awnlessness were detected in the landrace. Two of 18 Finnish landraces were found to carry accessory or B chromosomes in a study in 1964. B chromosomes are known to interfere with the expression of some genes, perhaps also ensuring variation in the vernalisation needs of the plants.

Inheritance of a Novel Heterozygous Peanut Mutant, 5-Small Leaflet

ABSTRACT An unusual 5-Small Leaflet mutant plant was found within the ‘Georgia Green' runner-type peanut (Arachis hypogaea L.) cultivar. Subsequent selfing has not established a true-breeding 5-Small Leaflet genotype. It continues to segregate normal and 5-Small Leaflet plants but with a reduced number of normal leaf plants upon selection for 5-Small Leaflet phenotypes after several self-generations. F1, F2, F3, and F4 data suggests that the 5-Small Leaflet trait is dominant or possibly pseudo-dominant. Likewise, the 5-Small Leaflet mutant can only be used as a pollen parent in crosses, and it has approximately a 1:1 ratio of elongated to normal stigmas, respectively, on individual plants. This is an example of a novel heterozygous peanut mutant plant found within the cultivated allotetraploid peanut.

Brain executive laterality and hemisity

Brain laterality refers to the asymmetric location of functional elements within the bilateral brain of animals and humans. Thus far, five lateralized functions have been recognized in humans: handedness, language ability, spatial skills, facial recognition, and emotion recognition. Recently, a sixth asymmetric functional element bearing on personality has been discovered. It is the larger side of the split bilateral anterior cingulate cortex (ACC). This appears to be the final output element of the executive system of which, by logic, there can be only one. Which side is somewhat larger varies among the general population in a seemingly idiosyncratic manner, yet with a genetic basis because true-breeding lineages exist. Here, hemisity is binary measure where a person is inherently born either right brain or left brain oriented. This is determined by nine statistically robust sets of four biophysical tests, none of which depend upon personality, and five behavioral questionnaires. Crucially these hemisity methods have been validated by the Magnetic Resonance Imaging (MRI)-based discovery that the larger side of the ACC is on the same side as one’s hemisity, making MRI the primary standard for hemisity determination (r = 0.96). There are at least 30 measurable differences in individual characteristics and behaviors between those persons whose hemsity is on the right compared to those with it on the left. The hemisity of 2929 individuals was determined by these methods. Large groups included 1428 junior and senior high schools students both in Hawaii and Utah. There were somewhat comparable numbers present for both types of hemisity. Hemisity of individuals was found stable from infancy to old age. There was no relation between hemisity and handedness. Larger corpus callosum (CC) size of male or female subjects was larger in right brainer that in left brainers. Twin studies demonstrate that CC size is inherited. Thirty-eight percent of individuals of both sexes were right brain oriented, while 62% of individuals of both sexes were left brain oriented. In pairings, there were more than twice as many couples with opposite hemisity. Of these couples, the right brain male and females were dominant. Reproductive outcomes of these were “Like father like son, Like mother like daughter.”

Improving accuracy of direct and maternal genetic effects in genomic evaluations using pooled boar semen: a simulation study1

Pooling semen of multiple boars is commonly used in swine production systems. Compared with single boar systems, this technique changes family structure creating maternal half-sib families. The aim of this simulation study was to investigate how pooling semen affects the accuracy of estimating direct and maternal effects for individual piglet birth weight, in purebred pigs. Different scenarios of pooling semen were simulated by allowing the same female to mate from 1 to 6 boars, per insemination, whereas litter size was kept constant (N = 12). In each pooled boar scenario, genomic information was used to construct either the genomic relationship matrix (G) or to reconstruct pedigree in addition to G. Genotypes were generated for 60,000 SNPs evenly distributed across 18 autosomes. From the 5 simulated generations, only animals from generations 3 to 5 were genotyped (N = 36,000). Direct and maternal true breeding values (TBV) were computed as the sum of the effects of the 1,080 QTLs. Phenotypes were constructed as the sum of direct TBV, maternal TBV, an overall mean of 1.25 kg, and a residual effect. The simulated heritabilities for direct and maternal effects were 0.056 and 0.19, respectively, and the genetic correlation between both effects was −0.25. All simulations were replicated 5 times. Variance components and direct and maternal heritability were estimated using average information REML. Predictions were computed via pedigree-based BLUP and single-step genomic BLUP (ssGBLUP). Genotyped littermates in the last generation were used for validation. Prediction accuracies were calculated as correlations between EBV and TBV for direct (accdirect) and maternal (accmat) effects. When boars were known, accdirect were 0.21 (1 boar) and 0.26 (6 boars) for BLUP, whereas for ssGBLUP, they were 0.38 (1 boar) and 0.43 (6 boars). When boars were unknown, accdirect was lower in BLUP but similar in ssGBLUP. For the scenario with known boars, accmat was 0.58 and 0.63 for 1 and 6 boars, respectively, under ssGBLUP. For unknown boars, accmat was 0.63 for 2 boars and 0.62 for 6 boars in ssGBLUP. In general, accdirect and accmat were lower in the single-boar scenario compared with pooled semen scenarios, indicating that a half-sib structure is more adequate to estimate direct and maternal effects. Using pooled semen from multiple boars can help us to improve accuracy of predicting maternal and direct effects when maternal half-sib families are larger than 2.