Challenges and Costs of Asexuality: Variation in Premeiotic Genome Duplication in Gynogenetic Hybrids from Cobitis taenia Complex.

The transition from sexual reproduction to asexuality is often triggered by hybridization. The gametogenesis of many hybrid asexuals involves premeiotic genome endoreplication leading to bypass hybrid sterility and forming clonal gametes. However, it is still not clear when endoreplication occurs, how many gonial cells it affects and whether its rate differs among clonal lineages. Here, we investigated meiotic and premeiotic cells of diploid and triploid hybrids of spined loaches (Cypriniformes: Cobitis) that reproduce by gynogenesis. We found that in naturally and experimentally produced F1 hybrids asexuality is achieved by genome endoreplication, which occurs in gonocytes just before entering meiosis or, rarely, one or a few divisions before meiosis. However, genome endoreplication was observed only in a minor fraction of the hybrid's gonocytes, while the vast majority of gonocytes were unable to duplicate their genomes and consequently could not proceed beyond pachytene due to defects in bivalent formation. We also noted that the rate of endoreplication was significantly higher among gonocytes of hybrids from natural clones than of experimentally produced F1 hybrids. Thus, asexuality and hybrid sterility are intimately related phenomena and the transition from sexual reproduction to asexuality must overcome significant problems with genome incompatibilities with a possible impact on reproductive potential.

Assessment of genetic divergence through cluster analysis of chilli varieties.

Our study on genetic diversity was conducted with six chilli genotypes with inter- and intra-specific cross varieties of the three most popular chilli species (Capsicum annuum L., Capsicum chinense Jacq., and Capsicum frutescens L.). Twelve quantitative characters, viz. plant height (cm), primary branches, secondary branches, number of flowers, number of fruits/plant; dry fruit weight (g), fruit length (cm), fruit diameter (cm), pedicel length (cm), pericarp thickness (mm), seeds/fruit, and seed weight (g), were taken into consideration. The analysis of variance revealed considerable variability among the genotypes for the character studied. Cluster analysis was used for grouping of parental and hybrid chilli genotypes under the study grouped into five clusters. Cluster I had the maximum (12) and clusters IVand V had the minimum number (1) of genotypes. The inter-cluster D2 values ranged between 40.404 and 127.530. The minimum inter-cluster distance was between clusters III and IV (40.404). The maximum inter-cluster distance was observed between clusters II and V (127.53). Diversity pattern and other horticultural performance among the genotypes of new varieties were generated due to the cross between Local Line Mahadev Pramanick and Sukhia bullet and also the cross between Local Line Mahadev Pramanick and Habanero orange (cluster II) as well as single parental variety i.e. Habanero orange. These genotypes were identified as promising varieties with respect to various characters may be taken into consideration as better parents for an efficient hybridization programme of chilli.

Reproductive performance of Angus, Hereford, Salers and Nellore crossbred females: Additive and non-additive effects.

Reproductive traits in breeding herds can be improved through crossbreeding, which results in breed differences, heterosis and breed complementarity. The aim of this study was to estimate group additive genetic and dominance effects for three reproductive traits; probability of artificial insemination (AIP); calving success (CS); and days to calving (DC) for Hereford (H), Angus (A), Nellore (N) and Salers (S) breeds under grazing conditions. Data were obtained from an experiment carried out during 1992-2002 by the Faculty of Agronomy, Universidad de la Republica (UdelaR), Uruguay and Caja Notarial de Seguridad Social. The data set contained reproductive information of 1,164 females from 11 different genetic groups (GG) consisting of crosses between H, N, S and A. AIP, CS and DC were examined in first-calf heifers, while CS and DC were examined in second-calf and 3- to 7-year-old cows. Least square means for each GG and group additive genetic and dominance effects were estimated for each trait. F1 crossbreed females performed better for artificial insemination probability than purebred females. Crossbred A/H heifers had the highest AIPs and CS rates, while crossbred N/H 3- to 7-year-old cows recorded the highest averages for CS and DC. Estimates of group additive genetic effects did not differ amongst A, S, N and H; however, dominance increased the AIP and CS of the heifers.

Assessment of Susceptibility of Outbred Albino Rats to the Formation of Depression-Like State of Learned Helplessness.

Learned helplessness (a model of depression-like state) was developed in rats by exposure to repeated inescapable electric stimulation and evaluated by the absence of attempts to escape when it could be performed. In randomly grouped outbred white rats, 37.5% animals after the above procedure meet the criterion of learned helplessness. On experimental day 14, the latent period and the number of applied electric shocks prior to the first escape to the safe compartment in rats with learned helplessness were significantly higher than in the control, but no significant differences in these parameters were observed on day 21. The Porsolt forced swimming test performed on days 14 and 21 revealed no differences from the control group. After the rats were divided into low- and high-active subgroups according to their open field behavior, 35% rats with learned helplessness were in the low-active subgroup group and 30% rats with learned helplessness were in the high-active subgroup. On day 14, the parameters of learned helplessness significantly surpassed the control levels only in the low-active subgroup. Only in rats with learned helplessness and low activity in the open field, the immobility time in the Porsolt test was longer than in control low-active rats. These findings attest to advisability of preliminary splitting of outbred animals by their open-field behavior into low- and high-active subgroups and the use of only animals for modeling learned helplessness.

The social supergene dates back to the speciation time of two Solenopsis fire ant species.

Colony social organization of multiple Solenopsis fire ant species is determined by a supergene with two haplotypes SB and Sb, which are similar to X/Y sex chromosomes. The ancestral monogyne (single-queen) social form has been associated with homozygous SB/SB queens, while queens in colonies with the derived polygyne (multi-queen) social structure are heterozygous SB/Sb. By comparing 14 Solenopsis invicta genomes and the outgroup S. fugax, we dated the formation of the supergene to 1.1 (0.7-1.6) million years ago, much older than previous estimates, and close to the estimated time of speciation of the two socially polymorphic species S. invicta and S. richteri. We also used 12 S. invicta and S. richteri genomes to compare the evolutionary distances between these species and the distances between the social haplotypes, and found them to be similar. A phylogenetic analysis suggested that the monophyletic Sb clade is more closely related to S. richteri SB haplotypes than to S. invicta SB haplotypes. We conclude that the formation of the supergene occurred concomitantly with the process of speciation of the Solenopsis socially-polymorphic clade, and hypothesize that the Sb variant first arouse in one incipiently-speciating population and then introgressed into the other populations or species.

Assessment of Genetic Heritability in Rice Breeding Lines Based on Morphological Traits and Caryopsis Ultrastructure.

Rice (Oryza sativa L) is a most important staple food crop of the world because more than half of the World's population is dependent on it for their livelihood. Global rice production must be doubled by 2050 to cope up with the situation of population growth. Narrow genetic base in the released varieties has made the improvement in plateaus. Widening the genetic base is necessary to overcome the yield barrier. Hybridization and pre-breeding has been carried out to broaden the genetic base. Heritability and genetic advances were measured in the F5 lines (Tulaipanji × IR64), F3 lines (Tulaipanji × IR64 × PB1460), and F3 lines (Badshabhog × Swarna sub1). Some of the breeding lines were showing promising field performance with high yield potentiality. Wide crosses were performed to widen the genetic base between (Ranjit × O. rufipogon) and (Badshabhog × O. rufipogon) and the heritability pattern of the morphological characteristics in the progeny lines was evaluated. Nutritional quality of the rice grain is totally dependent on the morphology and histological characteristics of the caryopsis which are genetically determined. Caryopses ultrastructural analyses were carried out in seventeen different rice breeding lines through SEM. SEM analysis showed distinguishing ultrastructure in respect to pericarp, testa, aleurone layer, protein bodies and starchy endosperm in the breeding lines with distinctive inheritance pattern. This study provides information about the cross compatibility of the wide hybridization and heritability measures of the morphological traits which may supplement the breeding program to break the yield plateaus.

Economics of reducing antibiotic usage for clinical mastitis and metritis through genomic selection.

Antibiotics use (ABU) in animal agriculture has been implicated in the emergence of antibiotic resistance, a global public health threat. Economically justifiable antibiotic reduction strategies can motivate farmers to reduce ABU for clinical mastitis (CM) and metritis, the most common reasons for ABU on dairy farms. Our objective was to quantify the reduction in incidence of CM, metritis, and ABU, and the herd performance of a representative US herd that uses genomic selection for Lifetime Net Merit 2018 (NM$) selection index, compared with genetic selection based only on the mastitis (MAST) or metritis resistance (METR) trait or a health trait subindex (HTH$). A stochastic dynamic simulation model of a 1,000-cow herd with multi-trait genetics for 19 correlated traits included in the NM$ affected the performance of animals. The incidence of CM and metritis for each animal was affected by the genetic and environmental components of the MAST or METR, along with a standard phenotypic function that calculated the daily underlying herd probability to contract CM or metritis. Selection decisions were made based on genomic estimated breeding values of the traits of interest. A strategy named AI-NM$ based decisions on the NM$ trait so that the correlated genetic trends in MAST and METR are improved. Three other strategies named AI-MAST, AI-METR, and AI-HTH$ maximized respectively MAST, METR, and HTH$ genetic merit, but with a tradeoff in NM$ genetic merit. The cumulative true breeding values (TBV) of NM$ for 15 yr showed a difference of $4,947 per cow between the AI-NM$ (best strategy for NM$) and AI-METR (worst strategy for NM$). However, the 15-yr cumulative TBV of MAST was 26.50 percentage points (PP) higher in AI-MAST, and 18.5 PP higher for METR in AI-METR, compared with AI-NM$. As a result, the 15-yr cumulative phenotypic CM and metritis incidence was respectively 94.03 PP and 58 PP lower in AI-MAST and AI-METR compared with AI-NM$. Therefore the corresponding 15-yr cumulative ABU decreased by 42% in AI-MAST and by 53% in AI-METR. We found that AI-MAST had the lowest CM incidence across the 15 yr, whereas AI-METR had the lowest incidence of metritis and the smallest total ABU for 15 yr. To achieve the lowest incidence of CM, metritis, and ABU strategies AI-MAST, AI-METR, and AI-HTH$ had to incur 15-yr discounted cumulative losses per cow of $1,486, $1,434, and $1,130, respectively, compared with AI-NM$. Hence, AI-NM$ had the best financial performance, despite having slightly higher incidence of CM, metritis, and ABU.

Gb8, a new gene conferring resistance to economically important greenbug biotypes in wheat.

KEY MESSAGE: A new greenbug resistance gene Gb8 conferring broad resistance to US greenbug biotypes was identified in hard red winter wheat line PI 595379-1 and was mapped to the terminal region of chromosome 7DL. Greenbug [Schizaphis graminum (Rondani)] is a worldwide insect pest that poses a serious threat to wheat production. New greenbug resistance genes that can be readily used in wheat breeding are urgently needed. The objective of this study was to characterize a greenbug resistance gene in PI 595379-1, a single plant selection from PI 595379. Genetic analysis of response to greenbug biotype E in an F2:3 population derived from a cross between PI 595379-1 and PI 243735 indicated that a single gene, designated Gb8, conditioned resistance. Linkage analysis placed Gb8 in a 2.7-Mb interval in the terminal bin of chromosome 7DL (7DL3-082-1.0), spanning 595.6 to 598.3 Mb in the Chinese Spring IWGSC RefSeq version 1.0 reference sequence. Gb8 co-segregated with a newly developed SSR marker Xstars508, positioned at 596.4 Mb in the reference sequence. Allelism tests showed that Gb8 was different from three permanently named genes on the same chromosome arm and the estimated genetic distance between Gb8 and Gb3 was 15.35 ± 1.35 cM. Gb8 can be directly used in wheat breeding to enhance greenbug resistance.

Construction, characteristics and high throughput molecular screening methodologies in some special breeding populations: a horticultural perspective.

Advanced marker technologies are widely used for evaluation of genetic diversity in cultivated crops, wild ancestors, landraces or any special plant genotypes. Developing agricultural cultivars requires the following steps: (i) determining desired characteristics to be improved, (ii) screening genetic resources to help find a superior cultivar, (iii) intercrossing selected individuals, (iv) generating genetically hybrid populations and screening them for agro-morphological or molecular traits, (v) evaluating the superior cultivar candidates, (vi) testing field performance at different locations, and (vii) certifying. In the cultivar development process valuable genes can be identified by creating special biparental or multiparental populations and analysing their association using suitable markers in given populations. These special populations and advanced marker technologies give us a deeper knowledge about the inherited agronomic characteristics. Unaffected by the changing environmental conditions, these provide a higher understanding of genome dynamics in plants. The last decade witnessed new applications for advanced molecular techniques in the area of breeding,with low costs per sample. These, especially, include next-generation sequencing technologies like reduced representation genome sequencing (genotyping by sequencing, restriction site-associated DNA). These enabled researchers to develop new markers, such as simple sequence repeat and single- nucleotide polymorphism, for expanding the qualitative and quantitative information onpopulation dynamics. Thus, the knowledge acquired from novel technologies is a valuable asset for the breeding process and to better understand the population dynamics, their properties, and analysis methods.

Ranking sires using genetic selection indices based on financial investment methods versus lifetime net merit.

Current USDA selection indices such as lifetime net merit (NM$) estimate lifetime profit differences, which are accurately approximated by a linear combination of 13 traits. In these indices, every animal gets credit for 2.78 lactations of the traits expressed per lactation, such as fat and protein, independent of its productive life (PL). This formulation may over- or underestimate the net revenue from traits expressed per lactation depending on PL. The objectives were to develop 2 genetic selection indices using financial investment methods to account for differences in PL and to compare them with the 2017 NM$ for marketed Holstein sires. Selection among animals with different PL is an example of investment in mutually exclusive projects that have unequal duration. Financial investment theory says that such projects are best compared with the annualized net present value (ANPV) method when replacement occurs with technologically equal assets. However, genetic progress implies that future available replacement animals are technologically improved assets. Asset replacement theory with improved assets results in an annualized value including genetic opportunity cost (AVOC) for each animal. We developed the ANPV and AVOC and compared these with the NM$ for 1,500 marketed Holstein sires from the December 2017 genetic evaluation. The lowest Pearson correlation coefficient was 0.980 between AVOC and NM$, whereas the highest was 0.999 between ANPV and NM$ among the 1,500 sires. Correlations for the top 300 sires were lower. Although we found high correlations between indices, the 95th and 5th percentiles of individual rank changes between AVOC and NM$ were +131 and -163 positions, respectively, whereas these changes between ANPV and NM$ were +27 and -45 positions, respectively. The relative emphasis of PL in the AVOC index was half of the relative emphasis in NM$. These results show that applying financial investment methods to value differences in genetic merit of animals changes their rankings compared with the NM$ formulation. Rank changes were meaningful enough that the new indices warrant consideration for use in practice.

Genotyping by low-coverage whole-genome sequencing in intercross pedigrees from outbred founders: a cost-efficient approach.

BACKGROUND: Experimental intercrosses between outbred founder populations are powerful resources for mapping loci that contribute to complex traits i.e. quantitative trait loci (QTL). Here, we present an approach and its accompanying software for high-resolution reconstruction of founder mosaic genotypes in the intercross offspring from such populations using whole-genome high-coverage sequence data on founder individuals (~ 30×) and very low-coverage sequence data on intercross individuals (< 0.5×). Sets of founder-line informative markers were selected for each full-sib family and used to infer the founder mosaic genotypes of the intercross individuals. The application of this approach and the quality of the estimated genome-wide genotypes are illustrated in a large F2 pedigree between two divergently selected lines of chickens. RESULTS: We describe how we obtained whole-genome genotype data for hundreds of individuals in a cost- and time-efficient manner by using a Tn5-based library preparation protocol and an imputation algorithm that was optimized for this application. In total, 7.6 million markers segregated in this pedigree and, within each full-sib family, between 10.0 and 13.7% of these were fully informative, i.e. fixed for alternative alleles in the founders from the divergent lines, and were used for reconstruction of the offspring mosaic genotypes. The genotypes that were estimated based on the low-coverage sequence data were highly consistent (> 95% agreement) with those obtained using individual single nucleotide polymorphism (SNP) genotyping. The estimated resolution of the inferred recombination breakpoints was relatively high, with 50% of them being defined on regions shorter than 10 kb. CONCLUSIONS: A method and software for inferring founder mosaic genotypes in intercross offspring from low-coverage whole-genome sequencing in pedigrees from heterozygous founders are described. They provide high-quality, high-resolution genotypes in a time- and cost-efficient manner. The software is freely available at https://github.com/CarlborgGenomics/Stripes .

Genomic selection for productive traits in biparental cassava breeding populations.

Cassava improvement using traditional breeding strategies is slow due to the species' long breeding cycle. However, the use of genomic selection can lead to a shorter breeding cycle. This study aimed to estimate genetic parameters for productive traits based on pedigree (pedigree and phenotypic information) and genomic (markers and phenotypic information) analyses using biparental crosses at different stages of selection. A total of 290 clones were genotyped and phenotyped for fresh root yield (FRY), dry matter content (DMC), dry yield (DY), fresh shoot yield (FSY) and harvest index (HI). The clones were evaluated in clonal evaluation trials (CET), preliminary yield trials (PYT), advanced yield trials (AYT) and uniform yield trials (UYT), from 2013 to 2018 in ten locations. The breeding stages were analyzed as follows: one stage (CET), two stages (CET and PYT), three stages (CET, PYT and AYT) and four stages (CET, PYT, AYT and UYT). The genomic predictions were analyzed via k-fold cross-validation based on the genomic best linear unbiased prediction (GBLUP) considering a model with genetic additive effects and genotype × location interactions. Genomic and pedigree accuracies were moderate to high (0.56-0.72 and 0.62-0.78, respectively) for important starch-related traits such as DY and FRY; when considering one breeding stage (CET) with the aim of early selection, the genomic accuracies ranged from 0.60 (DMC) to 0.71 (HI). Moreover, the correlations between the genomic estimation breeding values of one-stage genomic analysis and the estimated breeding values of the four-stage (full data set) pedigree analysis were high for all traits as well as for a selection index including all traits. The results indicate great possibilities for genomic selection in cassava, especially for selection early in the breeding cycle (saving time and effort).

Assessment of various genetic components through NCD-I and NCD-III designs of biparental mating in opium poppy.

Creation of genetic variability and development of varieties having higher yield potential depends on information about nature of gene action. The present investigation was undertaken to decipher the nature of gene action and allied genetic parameters involved in the inheritance of yield and yield-related component traits in opium poppy (Papaver somniferum L.). The biparental inbreeding progenies derived from four segregating base populations of crosses NB-1Kr40-3/3×NB-1Kr30+0.2-2/1, NB-5Kr40-7/2×58/1, NB-1Kr30+0.2-2/1×58/1 and NB-Kr40-3/3×NB-5Kr40-7/2 of opium poppy were analysed to study the gene actions involved in the inheritance of yield and component traits. Additive component of variance played a predominant role in North Carolina design (NCD)-I, while both additive and dominance genetic components were found important in NCD-III design. The presence of additive as well as nonadditive components of variance suggested that one or two generations of intermating in further generations followed by selection may lead to development of novel genotypes.

Assessment and Maintenance of Unigametic Germline Inheritance for C. elegans.

The recent work of Besseling and Bringmann (2016) identified a molecular intervention for C. elegans in which premature segregation of maternal and paternal chromosomes in the fertilized oocyte can produce viable animals exhibiting a non-Mendelian inheritance pattern. Overexpression in embryos of a single protein regulating chromosome segregation (GPR-1) provides a germline derived clonally from a single parental gamete. We present a collection of strains and cytological assays to consistently generate and track non-Mendelian inheritance. These tools allow reproducible and high-frequency (>80%) production of non-Mendelian inheritance, the facile and simultaneous homozygosis for all nuclear chromosomes in a single generation, the precise exchange of nuclear and mitochondrial genomes between strains, and the assessments of non-canonical mitosis events. We show the utility of these strains by demonstrating a rapid assessment of cell lineage requirements (AB versus P1) for a set of genes (lin-2, lin-3, lin-12, and lin-31) with roles in C. elegans vulval development.

Three-breed rotational crossbreds of Montbéliarde, Viking Red, and Holstein compared with Holstein cows for feed efficiency, income over feed cost, and residual feed intake.

Rotational 3-breed crossbred cows of Montbéliarde, Viking Red, and Holstein (CB) were compared with Holstein (HO) cows for alternative measures of feed efficiency as well as income over feed cost (IOFC) and residual feed intake (RFI) during the first 150 d of first, second, and third lactations. Primiparous and multiparous CB (n = 63 and n = 43, respectively) and HO (n = 60 and n = 37, respectively) cows were fed the same total mixed ration twice daily with refusals weighed once daily. Feed was analyzed for dry matter content, net energy for lactation, and crude protein content. Body weight (BW) was recorded twice weekly. Daily production of milk, fat, and protein were estimated from monthly test days with best prediction. Measures of efficiency from 4 to 150 d in milk (DIM) were feed conversion efficiency (FCE), defined as fat plus protein production (kg) per kilogram of dry matter intake (DMI); ECM/DMI, defined as kilograms of energy-corrected milk (ECM) per kilogram of DMI; net energy for lactation efficiency (NELE), defined as ECM (kg) per megacalorie of net energy for lactation intake; crude protein efficiency (CPE), defined as true protein production (kg) per kilogram of crude protein intake; and DMI/BW, defined as DMI (kg) per kilogram of BW. The IOFC was defined as revenue from fat plus protein production minus feed cost. The RFI from 4 to 150 DIM for each lactation was the residual error remaining from regression of DMI on milk energy output (Mcal), metabolic BW, and energy required for change in BW (Mcal). Statistical analysis of measures of feed efficiency and RFI for primiparous cows included the fixed effects of year of calving and breed group. For multiparous cows, statistical analysis included breed as a fixed effect and cow as a repeated effect nested within breed group. Primiparous CB cows had higher means for FCE (+5.5%), ECM/DMI (+4.0%), NELE (+4.0%), and CPE (+5.2%) and a lower mean DMI/BW (-5.3%) than primiparous HO cows. Primiparous CB cows ($875) also had higher mean IOFC than primiparous HO cows ($825). In addition, mean RFI from 4 to 150 DIM was significantly lower (more desirable) for primiparous CB cows than HO cows. Likewise, multiparous CB cows had higher means for FCE (+8.2%), ECM/DMI (+5.9%), NELE (+5.8%), and CPE (+8.1%) and a lower mean for DMI/BW (-4.8%) than multiparous HO cows. Multiparous CB cows ($1,296) also had a higher mean for IOFC than multiparous HO cows ($1,208) and a lower mean for RFI from 4 to 150 DIM than HO cows.

Ranking crop species using mixed treatment comparisons.

The mixed treatment comparison (MTC) method has been proposed to combine results across trials comparing several treatments. MTC allows coherent judgments on which of the treatments is the most effective. It produces estimates of the relative effects of each treatment compared with every other treatment by pooling direct and indirect evidence. In this article, we explore how this methodological framework can be used to rank a large number of agricultural crop species from yield data collected in field experiments. Our approach is illustrated in a meta-analysis of yield data obtained in 67 field studies for 36 different bioenergy crop species. The considered dataset defines a network of comparisons of crop species. We introduce several Bayesian MTC models based on baseline treatment contrasts and evaluate the practical advantages of these models to produce yield ratio estimates. We explore the consistency of some estimates by node-splitting and compare our results to those obtained with a classical two-way linear mixed model. Results reveal that the model showing the lowest deviance information criterion (DIC) includes both study random effects and study-specific residual variances. But all the tested models including study random effects lead to similar yield ratio estimates. The proposed Bayesian framework allows an in-depth analysis of the uncertainty in the species ranking.

Economic values and selection index in different Angus-Nellore cross-bred production systems.

Bioeconomic models were developed to calculate economic values (EV) for economically important traits in beef cattle, to evaluate the impact of these traits on production profitability, to assess possible market changes with a payment system and to develop economic selection indexes for Angus cattle for two production systems. Two beef cattle production systems were simulated as follows: a cow-calf cycle (CC) and a complete cycle (CoC). Following selection, positive changes in the EV were observed. In the CC, each 1.0% increment in weaning weight (WW), weaning rate (WR) and pregnancy rate (PR) resulted in increases in US$ 1.30, US$ 3.68 and US$ 3.55 per cow/year in profit, respectively. In the CoC, EV of US$ 1.01, US$ 1.79, US$ 1.19, US$ 1.34, US$ 6.84 and US$ 7.86 per cow/year were obtained for WW, year weight, yearling weight, final weight, WR and PR, respectively. The payment system for carcass quality showed that the scenario considering that 100% of the animals displayed uniform carcasses exhibited the highest EV and was considered optimal. Considering the sensitivity analysis, the price paid per animal was the factor that most affected the EV in both systems. The selection indexes obtained may be used in similar production systems, and the use of EV and selection indexes are important tools for any production system with positive change in profit after selection.

Consumer profile and acceptability of cooked beef steaks with edible and active coating containing oregano and rosemary essential oils.

Fresh animal products are highly perishable and characterized by a short shelf-life. Edible coatings with natural antioxidants (essential oils: EOs) could improve stability, ensure quality, and increase the shelf-life of fresh products. Due to the strong flavor of EOs, their use should consider consumer preferences and sensory acceptability. This study evaluated the effects of edible coating (with oregano and rosemary essential oil) on beef in relation to consumer preferences, besides the determination of habits of consumption and buying intentions of consumers. Acceptability scores from three clusters of consumers was described. Coating with oregano was the preferred. The higher consumer acceptance and willingness to buy this product indicate a great potential and possibility of using coatings with essential oils in fresh animal products.

Accounting for Errors in Low Coverage High-Throughput Sequencing Data When Constructing Genetic Maps Using Biparental Outcrossed Populations.

Next-generation sequencing is an efficient method that allows for substantially more markers than previous technologies, providing opportunities for building high-density genetic linkage maps, which facilitate the development of nonmodel species' genomic assemblies and the investigation of their genes. However, constructing genetic maps using data generated via high-throughput sequencing technology (e.g., genotyping-by-sequencing) is complicated by the presence of sequencing errors and genotyping errors resulting from missing parental alleles due to low sequencing depth. If unaccounted for, these errors lead to inflated genetic maps. In addition, map construction in many species is performed using full-sibling family populations derived from the outcrossing of two individuals, where unknown parental phase and varying segregation types further complicate construction. We present a new methodology for modeling low coverage sequencing data in the construction of genetic linkage maps using full-sibling populations of diploid species, implemented in a package called GUSMap. Our model is based on the Lander-Green hidden Markov model but extended to account for errors present in sequencing data. We were able to obtain accurate estimates of the recombination fractions and overall map distance using GUSMap, while most existing mapping packages produced inflated genetic maps in the presence of errors. Our results demonstrate the feasibility of using low coverage sequencing data to produce genetic maps without requiring extensive filtering of potentially erroneous genotypes, provided that the associated errors are correctly accounted for in the model.

Assessment and genetic analysis of heavy metal content in rice grain using an Oryza sativa × O. rufipogon backcross inbred line population.

BACKGROUND: Heavy metal accumulation in rice is a growing concern for public health. Backcross inbred lines derived from an interspecific cross of Oryza sativa × O. rufipogon were grown in two distinct ecological locations (Hangzhou and Lingshui, China). The objective of this study was to characterise the contents of heavy metal in rice grains, and to identify quantitative trait loci (QTLs) for heavy metal contents. RESULTS: The contents of Ni, As, Pb, Cr and Hg in milled rice showed a significant decline as compared with those in brown rice, whereas the content of Cd showed little change. The concentration of heavy metal in rice grain varied greatly between the two environments. A total of 24 QTLs responsible for heavy metal contents were detected, including two for both the brown and milled rice, 13 for brown rice only, and nine for milled rice only. All the QTLs except two had the enhancing alleles derived from O. rufipogon. Sixteen QTLs were clustered in six chromosomal regions. CONCLUSION: Environmental variation plays an important role in the heavy metal contents in rice grain. QTLs detected in this study might be useful for breeding rice varieties with low heavy metal content. © 2017 Society of Chemical Industry.