In this era of big data, breeding programs are producing ever larger amounts of data. This necessitates access to efficient management systems to keep track of cross, performance, pedigree, geographical and image-based data, as well as genotyping data. In this article, we report the progress on the Breeding Information Management System (BIMS), a free, secure and online breeding management system that allows breeders to store, manage, archive and analyze their private breeding data. BIMS is the first publicly available database system that enables individual breeders to integrate their private phenotypic and genotypic data with public data and, at the same time, have complete control of their own breeding data along with access to tools such as data import/export, data analysis and data archiving. The integration of breeding data with publicly available genomic and genetic data enhances genetic understanding of important traits and maximizes the marker-assisted breeding utility for breeders and allied scientists. BIMS incorporates the use of the Android App Field Book, open-source phenotype data collection software for phones and tablets that allows breeders to replace hard copy field books, thus alleviating the possibility of transcription errors while providing faster access to the collected data. BIMS comes with training materials and support for individual or small group training and is currently implemented in the Genome Database for Rosaceae, CottonGEN, the Citrus Genome Database, the Pulse Crop Database, and the Genome Database for Vaccinium. Database URLs: (https://www.rosaceae.org/), (https://www.cottongen.org/), (https://www.citrusgenomedb.org/), (https://www.pulsedb.org/) and (https://www.vaccinium.org/).

Crop breeding should be accelerated to address global warming and climate change. Wheat (Triticum aestivum L.) is a major food crop. Speed breeding (SB) and speed vernalization (SV) techniques for spring and winter wheat have recently been established. However, there are few practical examples of these strategies being used economically and efficiently in breeding programs. We aimed to establish and evaluate the performance of a breeder-friendly and energy-saving generation acceleration system by modifying the SV + SB system.

Understanding metapopulation dynamics requires knowledge about local population dynamics and movement in both space and time. Most genetic metapopulation studies use one or two study species across the same landscape to infer population dynamics; however, using multiple co-occurring species allows for testing of hypotheses related to different life history strategies. We used genetic data to study dispersal, as measured by gene flow, in three ambystomatid salamanders (Ambystoma annulatum, A. maculatum, and A. opacum) and the Central Newt (Notophthalmus viridescens louisianensis) on the same landscape in Missouri, USA. While all four salamander species are forest dependent organisms that require fishless ponds to reproduce, they differ in breeding phenology and spatial distribution on the landscape. We use these differences in life history and distribution to address the following questions: (1) Are there species-level differences in the observed patterns of genetic diversity and genetic structure? and (2) Is dispersal influenced by landscape resistance? We detected two genetic clusters in A. annulatum and A. opacum on our landscape; both species breed in the fall and larvae overwinter in ponds. In contrast, no structure was evident in A. maculatum and N. v. louisianensis, species that breed during the spring. Tests for isolation by distance were significant for the three ambystomatids but not for N. v. louisianensis. Landscape resistance also contributed to genetic differentiation for all four species. Our results suggest species-level differences in dispersal ability and breeding phenology are driving observed patterns of genetic differentiation. From an evolutionary standpoint, the observed differences in dispersal distances and genetic structure between fall breeding and spring breeding species may be a result of the trade-off between larval period length and size at metamorphosis which in turn may influence the long-term viability of the metapopulation. Thus, it is important to consider life history differences among closely related and ecologically similar species when making management decisions.

1. Cooperatively breeding species are typically long lived and hence, according to theory, are expected to maximize their lifetime reproductive success through maximizing survival. Under these circumstances, the presence of helpers could be used to lighten the effort of current reproduction for parents to achieve higher survival. 2. In addition, individuals of different sexes and ages may follow different strategies, but whether male and female breeders and individuals of different ages benefit differently from the presence of helpers has often been overlooked. Moreover, only one study that investigated the relationship between parental survival and the presence of helpers used capture-mark-recapture analyses (CMR). These methods are important since they allow us to account for the non-detection of individuals that are alive in the population but not detected, and thus, the effects on survival and recapture probability to be disentangled. 3. Here, we used multi-event CMR methods to investigate whether the number of helpers was associated with an increase in survival probability for male and female breeders of different ages in the sociable weaver Philetairus socius. In this species, both sexes reduce their feeding rate in the presence of helpers. We therefore predicted that the presence of helpers should increase the breeders' survival in both sexes, especially early in life when individuals potentially have more future breeding opportunities. In addition, sociable weaver females reduce their investment in eggs in the presence of helpers, so we predicted a stronger effect of helpers on female than male survival. 4. As expected we found that females had a higher survival probability when breeding with more helpers. Unexpectedly, however, male survival probability decreased with increasing number of helpers. This antagonistic effect diminished as the breeders grew older. 5. These results illustrate the complexity of fitness costs and benefits underlying cooperative behaviours and how these may vary with the individuals' sex and age. They also highlight the need for further studies on the sex-specific effects of helpers on survival.

Many plant processes depend on differential gene expression, which is generally controlled by complex proteins called transcription factors (TFs). In peach, 1533 TFs have been identified, accounting for about 5.5% of the 27,852 protein-coding genes. These TFs are the reference for the rest of the Prunus species. TF studies in Prunus have been performed on the gene expression analysis of different agronomic traits, including control of the flowering process, fruit quality, and biotic and abiotic stress resistance. These studies, using quantitative RT-PCR, have mainly been performed in peach, and to a lesser extent in other species, including almond, apricot, black cherry, Fuji cherry, Japanese apricot, plum, and sour and sweet cherry. Other tools have also been used in TF studies, including cDNA-AFLP, LC-ESI-MS, RNA, and DNA blotting or mapping. More recently, new tools assayed include microarray and high-throughput DNA sequencing (DNA-Seq) and RNA sequencing (RNA-Seq). New functional genomics opportunities include genome resequencing and the well-known synteny among Prunus genomes and transcriptomes. These new functional studies should be applied in breeding programs in the development of molecular markers. With the genome sequences available, some strategies that have been used in model systems (such as SNP genotyping assays and genotyping-by-sequencing) may be applicable in the functional analysis of Prunus TFs as well. In addition, the knowledge of the gene functions and position in the peach reference genome of the TFs represents an additional advantage. These facts could greatly facilitate the isolation of genes via QTL (quantitative trait loci) map-based cloning in the different Prunus species, following the association of these TFs with the identified QTLs using the peach reference genome.

The domestic cat (Felis catus) is a seasonal-breeding species whose reproductive period starts when the day length increases. Since the existing information on cat spermatogenesis is limited and somewhat contradictory, in the present study, germ cell proliferation and apoptosis in feral adult tomcats orchiectomized during reproductive (reproductive group, RG; February-July) and non-reproductive (non-reproductive group, NRG; November and December) seasons were compared. Cross-sections taken from the middle third of the left testis were chemically fixed and embedded in paraffin wax. Histological sections were processed for the immunohistochemical detection of proliferating germ cells (PCNA) and for the identification of apoptotic cells (TUNEL method). The percentage of PCNA-positive spermatogonia was higher in the RG than in the NRG. On the contrary, germ cell apoptosis was higher in the NRG than in the RG. Our results confirm that cat spermatogenesis is modulated on a seasonal basis and suggests that spermatogenesis control involves changes in germ cell proliferation and apoptosis according to a common paradigm of seasonally breeding species.

One of the biggest challenges for genetic studies on natural or unstructured populations is the unbalanced datasets where individuals are measured at different times and environments. This problem is also common in crop and animal breeding where many individuals are only evaluated for a single year and large but unbalanced datasets can be generated over multiple years. Many wheat breeding programs have focused on increasing bread wheat (Triticum aestivum L.) yield, but processing and end-use quality are critical components when considering its use in feeding the rising population of the next century. The challenges with end-use quality trait improvements are high cost and seed amounts for testing, the latter making selection in early breeding populations impossible. Here we describe a novel approach to identify marker-trait associations within a breeding program using a meta-genome wide association study (GWAS), which combines GWAS analysis from multi-year unbalanced breeding nurseries, in a manner reflecting meta-GWAS in humans. This method facilitated mapping of processing and end-use quality phenotypes from advanced breeding lines (n = 4,095) of the CIMMYT bread wheat breeding program from 2009 to 2014. Using the meta-GWAS we identified marker-trait associations, allele effects, candidate genes, and can select using markers generated in this process. Finally, the scope of this approach can be broadly applied in 'breeding-assisted genomics' across many crops to greatly increase our functional understanding of plant genomes.

This paper reviews and analyzes key features from cassava breeding at the International Center for Tropical Agriculture (CIAT) over 50 years and draws lessons for public breeding efforts broadly. The breeding team, jointly with national program partners and the private processing sector, defined breeding objectives and guiding business plans. These have evolved through the decades and currently focus on four global product profiles. The recurrent selection method also evolved and included innovations such as estimation of phenotypic breeding values, increasing the number of locations in the first stage of agronomic evaluations, gradual reduction of the duration of breeding cycles (including rapid cycling for high-heritability traits), the development of protocols for the induction of flowering, and the introduction of genome-wide predictions. The impact of cassava breeding depends significantly on the type of target markets. When roots are used for large processing facilities for starch, animal feeding or ethanol production (such as in SE Asia), the adoption of improved varieties is nearly universal and productivity at the regional scale increases significantly. When markets and relevant infrastructure are weak or considerable proportion of the production goes for local artisanal processing and on-farm consumption, the impact has been lower. The potential of novel breeding tools needs to be properly assessed for the most effective allocation of resources. Finally, a brief summary of challenges and opportunities for the future of cassava breeding is presented. The paper describes multiple ways that public and private sector breeding programs can learn from each other to optimize success.

The hormone prolactin has many diverse functions across taxa such as osmoregulation, metabolism, and reproductive behavior. In ring doves, central prolactin action is important for parental care and feeding behavior. However, there is a considerable lack of information on the distribution of the prolactin receptor (PRLR) in the avian CNS to test the hypothesis that prolactin mediates these and other functions in other birds. In order to advance this research, we collected brains from breeding and non-breeding zebra finches to map the PRLR distribution using immunohistochemistry. We found PRLRs are distributed widely across the brain, both in hypothalamic sites known to regulate parental care and feeding, but also in many non-hypothalamic sites, including the tectofugal visual pathway, song system regions, reward associated areas, and pallium. This raises the possibility that prolactin has other functions throughout the brain that are not necessarily related to feeding or parental care. In addition, we also stained brains for pSTAT5, a transcription factor which is expressed when the PRLR is activated and is used as a marker for PRLR activity. We found several notable differences in pSTAT5 activity due to the breeding state of the animal, in both directions, further supporting the hypothesis that prolactin has many diverse functions in the brain both within and outside times of breeding. Together, this study represents the first essential step to inform the design of causative studies which manipulate PRLR-expressing cells to test their role in a wide variety of behaviors and other physiological functions.

Recent advancements in genomic analysis technologies have opened up new avenues to promote the efficiency of plant breeding. Novel genomics-based approaches for plant breeding and genetics research, such as genome-wide association studies (GWAS) and genomic selection (GS), are useful, especially in fruit tree breeding. The breeding of fruit trees is hindered by their long generation time, large plant size, long juvenile phase, and the necessity to wait for the physiological maturity of the plant to assess the marketable product (fruit). In this article, we describe the potential of genomics-assisted breeding, which uses these novel genomics-based approaches, to break through these barriers in conventional fruit tree breeding. We first introduce the molecular marker systems and whole-genome sequence data that are available for fruit tree breeding. Next we introduce the statistical methods for biparental linkage and quantitative trait locus (QTL) mapping as well as GWAS and GS. We then review QTL mapping, GWAS, and GS studies conducted on fruit trees. We also review novel technologies for rapid generation advancement. Finally, we note the future prospects of genomics-assisted fruit tree breeding and problems that need to be overcome in the breeding.

Sorghum research has entered an exciting and fruitful era due to the genetic, genomic, and breeding resources that are now available to researchers and plant breeders. As the world faces the challenges of a rising population and a changing global climate, new agricultural solutions will need to be developed to address the food and fiber needs of the future. To that end, sorghum will be an invaluable crop species as it is a stress-resistant C4 plant that is well adapted for semi-arid and arid regions. Sorghum has already remained as a staple food crop in many parts of Africa and Asia and is critically important for animal feed and niche culinary applications in other regions, such as the United States. In addition, sorghum has begun to be developed into a promising feedstock for forage and bioenergy production. Due to this increasing demand for sorghum and its potential to address these needs, the continuous development of powerful community resources is required. These resources include vast collections of sorghum germplasm, high-quality reference genome sequences, sorghum association panels for genome-wide association studies of traits involved in food and bioenergy production, mutant populations for rapid discovery of causative genes for phenotypes relevant to sorghum improvement, gene expression atlas, and online databases that integrate all resources and provide the sorghum community with tools that can be used in breeding and genomic studies. Used in tandem, these valuable resources will ensure that the rate, quality, and collaborative potential of ongoing sorghum improvement efforts is able to rival that of other major crops.

High voltage-activated Cav2.3 R-type Ca2+ channels and low voltage-activated Cav3.2 T-type Ca2+ channels were reported to be involved in numerous physiological and pathophysiological processes. Many of these findings are based on studies in Cav2.3 and Cav3.2 deficient mice. Recently, it has been proposed that inbreeding of Cav2.3 and Cav3.2 deficient mice exhibits significant deviation from Mendelian inheritance and might be an indication for potential prenatal lethality in these lines. In our study, we analyzed 926 offspring from Cav3.2 breedings and 1142 offspring from Cav2.3 breedings. Our results demonstrate that breeding of Cav2.3 deficient mice shows typical Mendelian inheritance and that there is no indication of prenatal lethality. In contrast, Cav3.2 breeding exhibits a complex inheritance pattern. It might be speculated that the differences in inheritance, particularly for Cav2.3 breeding, are related to other factors, such as genetic specificities of the mutant lines, compensatory mechanisms and altered sperm activity.

Genotype × environment interaction (G × E) is of increasing importance for dairy cattle breeders due to international multiple-environment selection of animals as well as the differentiation of production environments within countries. This theoretical simulation study tested the hypothesis that genomic selection (GS) breeding programs realize larger genetic benefits by cooperation in the presence of G × E than conventional pedigree-based selection (PS) breeding programs. We simulated two breeding programs each with their own cattle population and environment. Two populations had either equal or unequal population sizes. Selection of sires was done either across environments (cooperative) or within their own environment (independent). Four scenarios, (GS/PS) × (cooperative/independent), were performed. The genetic correlation (r g ) between the single breeding goal trait expressed in two environments was varied between 0.5 and 0.9. We compared scenarios for genetic gain, rate of inbreeding, proportion of selected external sires, and the split-point r g that is the lowest value of r g for long-term cooperation. Between two equal-sized populations, cooperative GS breeding programs achieved a maximum increase of 19.3% in genetic gain and a maximum reduction of 24.4% in rate of inbreeding compared to independent GS breeding programs. The increase in genetic gain and the reduction in rate of inbreeding realized by GS breeding programs with cooperation were respectively at maximum 9.7% and 24.7% higher than those realized by PS breeding programs with cooperation. Secondly, cooperative GS breeding programs allowed a slightly lower split-point r g than cooperative PS breeding programs (0.85∼0.875 vs ≥ 0.9). Between two unequal-sized populations, cooperative GS breeding programs realized higher increase in genetic gain and showed greater probability for long-term cooperation than cooperative PS breeding programs. Secondly, cooperation using GS were more beneficial to the small population while also beneficial but much less to the large population. In summary, by cooperation in the presence of G × E, GS breeding programs realize larger improvements in terms of the genetic gain and rate of inbreeding, and have greater possibility of long-term cooperation than conventional PS breeding programs. Therefore, we recommend cooperative GS breeding programs in situations with mild to moderate G × E, depending on the sizes of two populations.

Seasonally breeding animals, such as green anole lizards (Anolis carolinensis), allow for the examination of the control of reproduction during different reproductive states. During the breeding season, the gonads are large and reproductively active. Following the breeding season, gonads regress and become less active, and the lizards enter a refractory period where breeding is inhibited. After this stage, a post-refractory period occurs during which the lizards are still in a non-breeding state, but environmental changes can trigger the onset of breeding. However, it is unclear what causes these changes in reproductive state and we hypothesized that this may be due to alterations in gonadotropin-releasing hormone (GnRH) signaling. The present study aimed to identify morphological and behavioral differences in GnRH- and saline-injected refractory and post-refractory male anoles when housed under the same non-breeding environmental conditions. We found that post-refractory anoles had increased testicular weight, recrudescence, sperm presence, and reproductive behavior, with no impact of GnRH injection. Renal sex segment size and steroidogenic acute regulatory protein (StAR) mRNA levels did not differ among groups, indicating that testosterone levels likely had not increased in post-refractory lizards. Post-refractory anoles in this study were beginning to transition towards a breeding state without exposure to changing environmental conditions, and GnRH was not necessary for these changes. These data reveal a complex interaction between the activation of breeding, changing environmental conditions, and the underlying physiology regulating reproduction in seasonally breeding lizards. Future studies are needed to further elucidate the mechanisms that regulate this relationship.

Plant breeders are supported by a range of tools that assist them to make decisions about the conduct or design of plant breeding programs. Simulations are a strategic tool that enables the breeder to integrate the multiple components of a breeding program into a number of proposed scenarios that are compared by a range of statistics measuring the efficiency of the proposed systems. A simulation study for the trait growth score compared two major strategies for breeding forage species, among half-sib family selection and among and within half-sib family selection. These scenarios highlighted new features of the QuLine program, now called QuLinePlus, incorporated to enable the software platform to be used to simulate breeding programs for cross-pollinated species. Each strategy was compared across three levels of half-sib family mean heritability (0.1, 0.5, and 0.9), across three sizes of the initial parental population (10, 50, and 100), and across three genetic effects models (fully additive model, a mixture of additive, partial and over dominance model, and a mixture of partial dominance and over dominance model). Among and within half-sib selection performed better than among half-sib selection for all scenarios. The new tools introduced into QuLinePlus should serve to accurately compare among methods and provide direction on how to achieve specific goals in the improvement of plant breeding programs for cross breeding species.

Advancements in -omics techniques provide powerful tools to assess the potential effects in composition of a plant at the RNA, protein and metabolite levels. These technologies can thus be deployed to assess whether genetic engineering (GE) causes changes in plants that go beyond the changes introduced by conventional plant breeding. Here, we compare the extent of transcriptome and metabolome modification occurring in leaves of four GE rice lines expressing Bacillus thuringiensis genes developed by GE and seven rice lines developed by conventional cross-breeding. The results showed that both types of crop breeding methods can bring changes at transcriptomic and metabolic levels, but the differences were comparable between the two methods, and were less than those between conventional non-GE lines were. Metabolome profiling analysis found several new metabolites in GE rice lines when compared with the closest non-GE parental lines, but these compounds were also found in several of the conventionally bred rice lines. Functional analyses suggest that the differentially expressed genes and metabolites caused by both GE and conventional cross-breeding do not involve detrimental metabolic pathways. The study successfully employed RNA-sequencing and high-performance liquid chromatography mass spectrometry technology to assess the unintended changes in new rice varieties, and the results suggest that GE does not cause unintended effects that go beyond conventional cross-breeding in rice.

The Japanese pear (Pyrus pyrifolia Nakai) is one of the most widely grown fruit trees in Japan, and it has been used throughout Japan's history. The commercial production of pears increased rapidly with the successive discoveries of the chance seedling cultivars 'Chojuro' and 'Nijisseiki' around 1890, and the development of new cultivars has continued since 1915. The late-maturing, leading cultivars 'Niitaka' and 'Shinko' were released during the initial breeding stage. Furthermore, systematic breeding by the Horticultural Research Station (currently, NARO Institute of Fruit Tree Science, National Agriculture and Food Research Organization (NIFTS)) began in 1935, which mainly aimed to improve fruit quality by focusing on flesh texture and black spot disease resistance. To date, 22 cultivars have been released, including 'Kosui', 'Hosui', and 'Akizuki', which are current leading cultivars from the breeding program. Four induced mutant cultivars induced by gamma irradiation, which exhibit some resistance to black spot disease, were released from the Institute of Radiation Breeding. Among these cultivars, 'Gold Nijisseiki' has become a leading cultivar. Moreover, 'Nansui' from the Nagano prefectural institute breeding program was released, and it has also become a leading cultivar. Current breeding objectives at NIFTS mainly combine superior fruit quality with traits related to labor and cost reduction, multiple disease resistance, or self-compatibility. Regarding future breeding, marker-assisted selection for each trait, QTL analyses, genome-wide association studies, and genomic selection analyses are currently in progress.

Phenotypic records of group means or group sums are a good alternative to individual records for some difficult to measure, but economically important traits such as feed efficiency or egg production. Accuracy of predicted breeding values based on group records increases with increasing relationships between group members. The classical way to form groups with more closely-related animals is based on pedigree information. When genotyping information is available before phenotyping, its use to form groups may further increase the accuracy of prediction from group records. This study analyzed two grouping methods based on genomic information: (1) unsupervised clustering implemented in the STRUCTURE software and (2) supervised clustering that models genomic relationships.

Increasing goose population sizes gives rise to conflicts with human socioeconomic interests and in some circumstances conservation interests. Grazing by high abundances of geese in grasslands is postulated to lead to a very short and homogeneous sward height negatively affecting cover for breeding meadow birds and impacting survival of nests and chicks. We studied the effects of spring grazing barnacle geese Branta leucopsis and brent geese Branta bernicla on occupancy of extensively farmed freshwater grasslands by nesting and brood-rearing waders on the island Mandø in the Danish Wadden Sea. We hypothesized that goose grazing would lead to a shorter grass sward, negatively affecting the field occupancy by territorial/nesting and chick-rearing waders, particularly species preferring taller vegetation. Goose grazing led to a short grass sward (<5 cm height) over most of the island. To achieve a variation in sward height, we kept geese off certain fields using laser light. We analyzed effects of field size, sward height, mosaic structure of the vegetation, proximity to shrub as cover for potential predators, and elevation above ground water level as a measure of wetness on field occupancy by nesting and chick-rearing waders. The analysis indicated that the most important factor explaining field occupancy by nesting redshank Tringa totanus, black-tailed godwit Limosa limosa, oystercatcher Haematopus ostralegus and lapwing Vanellus vanellus as well as by chick-rearing black-tailed godwit and lapwing was short vegetation height. Distance to shrub cover and elevation were less important. Hence, despite very intensive goose grazing, we could not detect any negative effect on the field occupancy by nesting nor chick-rearing waders, including redshank and black-tailed godwit, which are known to favor longer vegetation to conceal their nests and hide their chicks. Possible negative effects may be buffered by mosaic structures in fields and proximity to taller vegetation along fences and ditches.

Crop plant breeding involves selecting and developing new plant varieties with desirable traits such as increased yield, improved disease resistance, and enhanced nutritional value. With the development of high-throughput technologies, such as genomics, transcriptomics, and metabolomics, crop breeding has entered a new era. However, to effectively use these technologies, integration of multi-omics data from different databases is required. Integration of omics data provides a comprehensive understanding of the biological processes underlying plant traits and their interactions. This review highlights the importance of integrating omics databases in crop plant breeding, discusses available omics data and databases, describes integration challenges, and highlights recent developments and potential benefits. Taken together, the integration of omics databases is a critical step towards enhancing crop plant breeding and improving global food security.