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PubMed2026

Engineering cold stress resilience in capsicum annuum through functional genomics and precision breeding.

This review synthesizes the molecular mechanisms of cold tolerance in pepper, integrating multi-omics data,genome editing, and precision breeding strategies to accelerate the development of cold-resilient cultivars. Cold stress is a significant environmental factor that affects the growth, productivity, and fruit quality of Capsicum annuum by impairing membrane integrity photosynthesis and cellular redox homeostasis. Although pepper has several endogenous cold-responsive regulators such as CaNAC035 and CabHLH035, along with antioxidant defense systems, its cold tolerance remains limited due to low transcriptional activation of key regulators, functional redundancy among cold-responsive genes, and the polygenicity of cold tolerance. These complexities, combined with low genetic diversity and linkage drag, have hindered the improvement of cold-resistant cultivars through conventional breeding. This review brings together the recent progress in understanding the molecular mechanisms of cold stress perception, signal transduction, transcriptional regulation, metabolic reprogramming, and phytohormone interactions in pepper. Precision Breeding 2.0 is a new innovation that combines the integration of multi-omics-based target identification with next-generation genome-editing techniques, allowing precise and multiplex engineering of complex and interconnected regulatory networks instead of single genes. We cover new approaches such as engineering the DREB/CBF pathway, allele-specific editing and targeted disruption of negative regulators to enhance the pathway(s) involved in cold response. Moreover, we propose a roadmap for integration of transcriptomics, proteomics, metabolomics, high-throughput phenomics, and speed breeding to accelerate the identification, validation, and deployment of superior alleles to boost cold tolerance. This review provides a foundation for developing climate-resilient pepper cultivars by connecting functional genomics with precision genome engineering approaches to maintain productivity under variable environmental conditions.

Capsicum↗

PubMed2026

Translating Flood-Tolerance Biology into Breeding: A 5D Framework for Next-Generation Rice Varieties.

Flooding is among the most devastating abiotic stresses limiting rice productivity. Although SUB1A introgression conferred submergence tolerance in several mega-varieties, this single-gene approach is insufficient for the diverse flood types-flash floods, stagnant floods, anaerobic germination, and deepwater inundation-progressively intensifying with climate change. Here, we review the physiological mechanisms and genetic architecture underlying tolerance to each flood type, emphasizing the dual role of reactive oxygen species (ROS) in signalling and damage, the management of elemental toxicities (Fe2+, Mn2+) under altered soil redox, and lessons from wetland species and lowland rice. We then examine why marker-assisted selection has failed for polygenic, multi-stress tolerance and identify persistent breeding bottlenecks. Building on this biological foundation, we outline an integrated 5D framework (Demand, Discovery, Design, Development, Deployment) that links gene-bank diversity, multi-omics discovery, predictive breeding and on-farm validation through continuous feedback. We discuss how connected breeding, the transition-from-trait-to-environment (TTE) strategy, and speed breeding can accelerate genetic gain, and we close with research priorities centred on the biology of multi-flood tolerance to develop climate-resilient rice.

5D breeding framework↗

PubMed1995

Effect of changing from a short-day to long-day photoperiod on the breeding season of the brushtail possum (Trichosurus vulpecula).

In Queensland, possums (Trichosurus vulpecula) in the wild and in captivity first give birth during March and April and continue to give birth throughout the year until November. The possum has a gestation length of 17.5 days, gives birth to one young, and lactation continues for approximately 180 days. If the newborn possum is removed during the breeding season, the possum will ovulate approximately 9 days later and give birth approximately 26 days after removal of the pouch young (RPY). Repeated RPY may be used to determine the duration of the breeding season. In this study, the effect on the breeding season of a marked change in photoperiod From a short-day to a long-day was examined by comparing three groups of possums in different photoperiods for 13 months. One group of five female and two mail possums (group A) was housed in a natural photoperiod and a second group (B) was housed in a short-day photoperiod (10 h light: 14 h dark) throughout the study. The third group (C) was housed in a short-day photoperiod until each possum gave birth, the pouch young was removed, and the possum transferred to a long-day photoperiod room (14 h light: 10 h dark) for the remainder of the study. The possums held in a natural photoperiod, group A, gave birth to a total of 27 births in the one breeding season from March to October.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗

PubMed1993

Plasma prolactin during the breeding season in adult and immature macaroni (Eudyptes chrysolophus) and gentoo (Pygoscelis papua) penguins.

Plasma prolactin levels were measured in free-living breeding adult and immature (pre-breeding) macaroni (Eudyptes chrysolophus) and gentoo (Pygoscelis papua) penguins at Bird Island, South Georgia (54 degrees S, 38 degrees W). Macaroni and gentoo penguins first breed at 5-6 and 2 years of age, respectively. In adult birds, of both species, prolactin was low (< 1.0 microgram. liter-1) during the courtship period and then increased during early (gentoo) to mid (macaroni) incubation (to 3.9-4.7 and 2.4-3.5 micrograms.liter-1, respectively), remaining elevated until the creche period, by which time continuous nest attendance by the adults had ceased. This pattern is similar to that seen in other altricial species and is consistent with delayed onset of brood patch development and full incubation efficiency, which has been previously reported in penguins. Adult female macaroni penguins showed a marked, but transient, increase in prolactin concentrations within 24 hr of the first egg being laid (from 1.7 to 7.0 micrograms.liter-1), plasma levels decreasing following clutch completion (to prelaying levels) before increasing again during incubation. Elevated plasma prolactin levels occurred in all age classes of immature (nonbreeding) birds in both macaroni (1- to 5 year-olds) and gentoo (1-year-olds) penguins. However, compared to that in adult birds, the increase in prolactin was more transient in immatures, a smaller proportion of immatures had detectable prolactin levels at each stage of the breeding cycle, and, at least in 1- and 2-year-olds, absolute levels of prolactin were lower.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗

PubMed1998

Prolactin receptor gene expression in the brain and peripheral tissues in broody and nonbroody breeds of domestic hen.

The objective of this study was to establish whether the gene encoding prolactin receptor (PRLR) is expressed in the hypothalamus and peripheral tissues of the domestic chicken and, if so, to determine whether there are breed differences in the structure or expression of the gene which might account for the observation that broodiness does not occur in the White Leghorn hen but does occur in other breeds of domestic hens, including the bantam. A preliminary experiment demonstrated that the absence of broodiness in White Leghorns is not due to a lack of a prolactin response to the avian prolactin-releasing hormone vasoactive intestinal polypeptide. The largest amounts of PRLR mRNA in the brain, which did not differ significantly between laying White Leghorns and bantams, were found in the pituitary gland and basal and preoptic hypothalamus. Small or nondetectable amounts were found in both breeds in the forebrain, cerebellum, and optic lobes. Prolactin receptor mRNA was widely distributed in peripheral tissues in both breeds, in the following descending order of abundance: kidney, leg skin, brood patch, duodenum, intestine > thyroid gland > adrenal gland, liver, ovary >> adipose tissue > thymus, spleen > muscle > blood. Southern blotting analysis using four restriction enzymes and a chicken PRLR cDNA probe demonstrated identical digestion patterns for White Leghorn and bantam genomic DNA. Northern blotting analysis identified two sizes of chicken PRLR mRNA transcripts (7.5 and 3.3 kb) in hypothalami from laying White Leghorn and bantam hens. It is concluded that differences in the expression of broodiness in White Leghorn and bantam hens cannot be explained by differences in the amounts of PRLR mRNA in the hypothalamus or in the transcription or gross structure of the PRLR gene.

Animals↗

PubMed1997

Persistence and evolution of feline coronavirus in a closed cat-breeding colony.

Feline coronavirus (FCoV) persistence and evolution were studied in a closed cat-breeding facility with an endemic serotype I FCoV infection. Viral RNA was detected by reverse transcriptase polymerase chain reaction (RT-PCR) in the feces and/or plasma of 36 of 42 cats (86%) tested. Of 5 cats, identified as FCoV shedders during the initial survey, 4 had detectable viral RNA in the feces when tested 111 days later. To determine whether this was due to continuous reinfection or to viral persistence, 2 cats were placed in strict isolation and virus shedding in the feces was monitored every 2-4 days. In 1 of the cats, virus shedding continued for up to 7 months. The other animal was sacrificed after 124 days of continuous virus shedding in order to identify the sites of viral replication. Viral mRNA was detected only in the ileum, colon, and rectum. Also in these tissues, FCoV-infected cells were identified by immunohistochemistry. These findings provide the first formal evidence that FCoV causes chronic enteric infections. To assess FCoV heterogeneity in the breeding facility and to study viral evolution during chronic infection, FCoV quasispecies sampled from individual cats were characterized by RT-PCR amplification of selected regions of the viral genome followed by sequence analysis. Phylogenetic comparison of nucleotides 7-146 of ORF7b to corresponding sequences obtained for independent European and American isolates indicated that the viruses in the breeding facility form a clade and are likely to have originated from a single founder infection. Comparative consensus sequence analysis of the more variable region formed by residues 79-478 of the S gene revealed that each cat harbored a distinct FCoV quasispecies. Moreover, FCoV appeared to be subject to immune selection during chronic infection. The combined data support a model in which the endemic infection is maintained by chronically infected carriers. Virtually every cat born to the breeding facility becomes infected, indicating that FCoV is spread very efficiently. FCoV-infected cats, however, appear to resist superinfection by closely related FCoVs.

Amino Acid Sequence↗

PubMed1993

Characterization of 24 porcine (dA-dC)n-(dT-dG)n microsatellites: genotyping of unrelated animals from four breeds and linkage studies.

Twenty-four PCR primer pairs were designed for the detection of porcine microsatellites. Polymorphism was investigated in 76 unrelated animals from four different breeds: Duroc, Landrace, Hampshire, and Yorkshire. Compared with human microsatellites, a general lower heterozygosity was detected; however, for each microsatellite a significant variation between breeds in number of alleles and heterozygosity was seen. Mean heterozygosity was found to be significantly higher (P < 0.01%) in the Yorkshire breed than in the other three breeds. Linkage analyses with the CEPH linkage packet were performed in a backcross family comprising 45 animals, of which 43 had informative meioses. Ten of the microsatellites could be assigned to six different linkage groups, demonstrating that linkage mapping with microsatellites can be carried out with great efficiency in a relatively small number of animals. Four of the linkage groups represent Chromosomes (Chrs) 4, 6, 7, and 8 respectively, while two linkage groups are unassigned.

Alleles↗

PubMed1981

A genetic study of bovine lymphocyte antigens (BoLA) and their frequency in several breeds.

Using sera which defined the BoLA specificities at the two International BoLA workshops (Edinburgh, 1978 and Wageningen, 1980) and the European Regional workshop (Paris, 1979), 142 informative matings from 15 bulls have been studied. On the basis of this data, 11 of the 15 internationally agreed specificities and one of the regionally defined specificities behave as if controlled by alleles at a single autosomal locus. Data has not as yet been obtained for the other four internationally agreed specificities which are also believed to be at this locus. - The frequencies of 13 of the internationally agreed specificities and one of the regionally defined specificities have been studied for both sexes in one breed and for a single sex in another five breeds. The other two internationally agreed specificities are very recent and the populations have not been tested for them. The frequencies between sexes within a breed and within sexes between breeds differ significantly.

Alleles↗

PubMed1993

Host resistance to ticks (Acari: Ixodidae) in different breeds of cattle at Bako, Ethiopia.

European cattle breeds are being introduced into Ethiopia in an effort to improve the productivity of indigenous breeds. The Ethiopian cattle breeds Horro and Boran were compared for tick burdens with their crosses with Friesian, Jersey and Simmental. Horro animals had the lowest tick burdens and the Horro x Friesian the highest. Adaptation to their environment and long-term natural selection for tick resistance in Horro cattle is the most likely explanation. Repeatability of tick burdens in all animals considered as one herd were only statistically significant for Boophilus decoloratus, the most abundant tick species. Statistically significant correlations between burdens of female B. decoloratus, Amblyomma cohaerens and Rhipicephalus praetextatus were observed and the addition of the males resulted in all inter-species correlations becoming significant. Care should be taken when crossing Ethiopian with more productive European cattle breeds in order not to lower their tick and disease resistance.

Adaptation, Physiological↗

PubMed2003

Testing for linkage disequilibrium in the New Zealand radiata pine breeding population.

Linkage analysis is commonly used to find marker-trait associations within the full-sib families of forest tree and other species. Study of marker-trait associations at the population level is termed linkage-disequilibrium (LD) mapping. A female-tester design comprising 200 full-sib families generated by crossing 40 pollen parents with five female parents was used to assess the relationship between the marker-allele frequency classes obtained from parental genotypes at SSR marker loci and the full-sib family performance (average predicted breeding value of two parents) in radiata pine ( Pinus radiata D. Don). For alleles (at a marker locus) that showed significant association, the copy number of that allele in the parents was significantly correlated, either positively or negatively, with the full-sib family performance for various economic traits. Regression of parental breeding value on its genotype at marker loci revealed that most of the markers that showed significant association with full-sib family performance were not significantly associated with the parental breeding values. This suggests that over-representation of the female parents in our sample of 200 full-sib families could have biased the process of detecting marker-trait associations. The evidence for the existence of marker-trait LD in the population studied is rather weak and would require further testing. The exact test for genotypic disequilibrium between pairs of linked or unlinked marker loci revealed non-significant LD. Observed genotypic frequencies at several marker loci were significantly different from the expected Hardy-Weinberg equilibrium. The possibilities of utilising marker-trait associations for early selection, among-family selection and selecting parents for the next generation of breeding are also discussed.

Breeding↗

PubMed2004

Open-nucleus breeding strategies compared with population-wide positive assortative mating: I. Equal distribution of testing efforts.

Positive assortative mating (PAM) can enhance the additive genetic variance in a breeding population(BP). This increases the potential for gains in the production population (PP, selected subset of the BP) for recurrent selection programs in forest trees. The assortment of mates can be either: (1) by individual tree rank across the whole BP (PAM), or (2) trees of similar rank can be merged into larger hierarchical groups and then mated randomly within group ("open"-nucleus breeding,NB). The objective of this study was to compare PAM and NB in quantitative terms. The NB simulation model assumed two tiers (nucleus, main) with unrestricted migration between the tiers. Clonal tests were used to predict breeding values and test resources per mate were kept constant for all mates. Both gain and diversity were combined into a single selection criterion, "group-merit selection." Alternatives were compared over five breeding cycles by considering genetic gain and diversity in a selected PP established in a seed orchard. The assortment of mates in both alternatives enhanced additive variance and increased the additive effect in the BP, leading to additional gain in the PP. Gains generated under PAM always exceeded gains under NB. Thus, the main message from this study is that PAM in both the short- and long-term results in more gain at any target level of diversity in the PP (the breeder's target) than is achieved by the NB alternative. The optimum size of the nucleus varies with the desired level of seed orchard diversity. At lower target diversity, smaller nucleus sizes are favorable, while larger sizes result in more gain when seed orchard diversity is considered more important.

Breeding↗

PubMed2006

Dot-blot-SNP analysis for practical plant breeding and cultivar identification in rice.

We report dot-blot hybridization with allele-specific oligonucleotides for single nucleotide polymorphisms (SNPs) analysis to be applicable for practical plant breeding and cultivar identification. Competitive hybridization of a digoxigenin-labeled oligonucleotide having the sequence of a mutant allele (or a wild-type allele) together with an unlabeled oligonucleotide having the sequence of a wild-type allele (or a mutant allele) was highly effective to reduce background signals in dot-blot hybridization. All 100 tested genes (200 alleles) in rice having SNPs or insertions/deletions were detected in an allele-specific manner. Genotypes of 43 rice cultivars were identified by this technique, and eight SNP markers were found to be sufficient for distinguishing all the cultivars from each other. Dot-blot analysis was also applied to genotyping of Wx and Sd1 of F4 plants in a conventional breeding program. Since dot-blot analysis with competitive hybridization provides a highly reliable, simple, and cost-effective technique for SNP analysis of a large number of samples, this technique is expected to realize the practical use of a novel breeding method, in which plants or breeding lines are selected by SNP analyses of many genes in a laboratory.

Alleles↗

PubMed2006

Mind the gap: analysis of marker-assisted breeding strategies for inbred mouse strains.

The development of congenic mouse strains is the principal approach for confirming and fine mapping quantitative trait loci, as well as for comparing the phenotypic effect of a transgene or gene-targeted disruption between different inbred mouse strains. The traditional breeding scheme calls for at least nine consecutive backcrosses before establishing a congenic mouse strain. Recent availability of genome sequence and high-throughput genotyping now permit the use of polymorphic DNA markers to reduce this number of backcrosses, and empirical data suggest that marker-assisted breeding may require as few as four backcrosses. We used simulation studies to investigate the efficiency of different marker-assisted breeding schemes by examining the trade-off between the number of backcrosses, the number of mice produced per generation, and the number of genotypes per mouse required to achieve a quality congenic mouse strain. An established model of crossover interference was also incorporated into these simulations. The quality of the strain produced was assessed by the probability of an undetected region of heterozygosity (i.e., "gaps") in the recipient genetic background, while maintaining the desired donor-derived interval. Somewhat surprisingly, we found that there is a relatively high probability for undetected gaps in potential breeders for establishing a congenic mouse strain. Marker-assisted breeding may decrease the number of backcross generations required to generate a congenic strain, but only additional backcrossing will guarantee a reduction in the number and length of undetected gaps harboring contaminating donor alleles.

Animals↗

PubMed2026

Genomic analysis of breed composition and population structure in Montana composite cattle.

The Montana composite was developed in Brazil from crosses between Bos indicus and Bos taurus and structured into four biological types: Zebu (N), adapted taurine (A), British taurine (B), and continental taurine (C). This study aimed to characterize the genetic diversity and population structure of the Montana composite using genomic data through principal component analysis (PCA), admixture analysis, and Wright's FST statistic. The PCA revealed a clear separation between Bos indicus and Bos taurus groups, with Montana animals distributed in an intermediate position. The first two principal components explained 69.48% and 3.45% of the total variation, respectively. Supervised admixture estimates indicated a predominance of taurine contribution, with type A accounting for 34.47%, 52.64%, and 51.71% at K = 4, 9, and 11, respectively. Increasing the ancestry resolution refined the contribution of individual founder breeds without changing the overall predominance of taurine ancestry. Comparisons between breed proportions obtained from pedigree and genomic data revealed significant differences, for most biological types and ancestry models (P < 0.001), indicating that realized breed composition deviates from theoretical expectations. Estimates of genetic differentiation confirmed greater divergence between Zebu and taurine groups, as well as reduced distances among populations sharing common ancestry. Specific relationships were identified between the composite and some of its founder breeds, particularly Belmont Red, Senepol, and Tuli. Overall, the results demonstrate that the Montana composite has a complex genomic structure, with genomic ancestry varying according to the resolution adopted and differing from pedigree-based expectations.

Animals↗

PubMed2003

Nutritional quality of prebreeding diet influences breeding performance of the Florida scrub-jay.

Food supplementation studies of breeding birds have traditionally concentrated on energetic constraints on breeding performance. It is only recently that the nutritional quality of the prebreeding diet has also been considered influential. We examined the importance of specific nutrients in the prebreeding diet of the Florida scrub-jay ( Aphelocoma coerulescens). Birds were provided with one of two supplements (rich in protein and fat or rich in fat only) prior to breeding in 2000 and 2001 and their breeding performance, in relation to unsupplemented (control) birds, was examined. Birds receiving both supplements significantly advanced laying in both years, and increased clutch size in 2000 but not in 2001. Laying date explained variation in clutch size in birds on dietary supplements. Egg mass and volume declined with laying order, irrespective of dietary treatment, but birds on the high fat, high protein diet laid heavier third eggs than controls and this was independent of laying date. Laboratory analysis of 14 abandoned and unhatched eggs revealed that as egg mass increased so did the absolute amount of protein and water while fat content remained relatively fixed. Using these relationships between the masses of egg components and fresh egg mass, we calculated that heavier third eggs laid by birds on high fat and high protein, compared with those laid by controls, contained more water that may be fundamental to chick growth and survival. This is the first demonstration for an avian species that nutritional quality of prebreeding diet can simultaneously influence laying date, clutch size, and egg size and composition.

Animal Feed↗

PubMed1977

Structure of northern elephant seal population breeding on San Nicholas Island, California, in 1971.

The structure of the population of northern elephant seals, Mirounga angustirostris, on San Nicolas Island, California, was studied during the 1970 and 1971 breeding season. At the population peak on 31 January 1971, there were 77 males, 306 females, 315 pups, and 6 yearlings on shore. The breeding population was subdivided into 15 groups, containing from 3 to 75 breeding animals. Fourteen of the groups were considered territories defended by individual males, and one group, the largest, was controlled by three males in a social hierarchy. The relatively small size of the San Nicolas population and the large amount of available beach space allowed the existence of numerous small breeding groups. Female elephant seals, although gregarious, apparently prefer to be in small groups when conditions permit it. It is likely that the same males that were territorial would have formed the nucleus of a social hierarchy if space had been limited enough to cause all of the females in the population to congregate in one large group.

Animals↗

PubMed2006

Breed effect on early cytokine mRNA expression in spleen and cecum of chickens with and without Salmonella enteritidis infection.

We examined mRNA expression of 11 genes: BAK, Bcl-x, Interferon [IFN]-gamma, Interleukin [IL]-1beta, IL-6, IL-10, IL-12alpha, IL-12beta, IL-18, CXCLi2 [IL-8/CAF], and a MIP family chemokine, CCLi2, in the spleen and cecum of day-old chicks after oral inoculation with Salmonella enteritidis (SE) or medium. Three distinct chicken breeds (broiler, Fayoumi, and Leghorn) were evaluated for mRNA expression levels at 2 and 18h post-inoculation using quantitative reverse transcriptase-polymerase chain reaction (RT-PCR). SE exposure significantly increased splenic IL-18 and IFN-gamma expression. Breed effect was significant (P<0.05) for CXCLi2, IL-10, IL-12alpha, and CCLi2 mRNA expression in the spleen, and for IL-12alpha, IL-12beta, IL-18, and CCLi2 mRNA expression in the cecum. Generally, mRNA expression levels were higher in the spleen, and lower in the cecum, of Leghorns versus broilers. These results support a role for breed genetics influencing cytokine mRNA expression in young chickens and may potentially explain some generalized immune response differences between breeds.

Animals↗

PubMed2005

Effect of breed and age on sexual behaviour of rams.

The objective of this study was to highlight the problems that arise during the reproduction between thin-tailed rams and fat-tailed ewes. At the same time, particular emphasis laid on the influence of sheep breed, sheep age, time after ram introduction and day of the ewe estrus cycle on ram and ewe sexual behaviour. Rams were subjected to sexual performance tests by being individually exposed to 12 ewes for 3 h daily, 19 consecutive days. The 16 rams of the experiment were separated according to their age (9 and 21 months old) and breed (Chios and Karagouniki), and the 96 ewes of Chios fat-tailed breed, were divided by age (9 and 21 months old). The main characteristics of courtship behaviour, like sniffing, nudging, flehmen response and following were recorded and studied in detail. Mature Chios rams, which were the only one with previous experience of Chios ewes, exhibited higher rates of sexual interest per ewe than the other rams (P < 0.05). On the other hand, rams sniffed and nudged more young than mature ewes (P < 0.05), probably due to the fact that young ewes did not express intense symptoms of estrus. Young rams exhibited substandard sexual interest towards mature ewes, when they first came in contact with them (P < 0.05). In general, Karagouniki thin-tailed rams exhibited reduced rates of mating behaviour when they courted with Chios fat-tailed ewes in comparison with Chios rams (P < 0.05). Moreover, as the time after ram introduction passed, the frequency and duration of sexual behaviour components decreased (P < 0.001). Finally, the effect of the day of the experiment was only significant in the case of sniffing, which increased during the first 2 days and then declined and stabilized (P < 0.01). As it was demonstrated, ram age and ram breed played a fundamental role in the exhibition of sexual interest elements.

Age Factors↗