Breeding Cycle Research Articles

A Study on the Development of a Predictive Model for the Number of Korean Cattle using a Sine Function

Due to the biological characteristics of Korean beef cattle, the breeding period is long, so the number of breeding heads repeats increase and decrease. So they have a certain breeding cycle. In this study, we develop a model using a sine function that can reflect these characteristics of the Korean breeding cycle. Recently, the Korean beef cattle industry is undergoing structural changes such as scale-up, specialization, and increase in integrated breeding, and this has been reflected in the model. The explanatory power of the model was 0.92, which was very high, and the MAPE was 2.38%, indicating that the model had excellent predictive power. As a result of forecasting the number of Korean beef cattle, it is predicted that it will gradually increase from 3.4 million in 2021, reach the maximum level of about 3.85 million in 2026, and then decrease. The results of this study are expected to be useful for resolving the supply and demand instability in the Korean beef cattle market and the management risk of farms.

Strategies of preserving genetic diversity while maximizing genetic response from implementing genomic selection in pulse breeding programs

Key messageGenomic selection maximizes genetic gain by recycling parents to germplasm pool earlier and preserves genetic diversity by restricting the number of fixed alleles and the relationship in pulse breeding programs.Using a stochastic computer simulation, we investigated the benefit of optimization strategies in the context of genomic selection (GS) for pulse breeding programs. We simulated GS for moderately complex to highly complex traits such as disease resistance, grain weight and grain yield in multiple environments with a high level of genotype-by-environment interaction for grain yield. GS led to higher genetic gain per unit of time and higher genetic diversity loss than phenotypic selection by shortening the breeding cycle time. The genetic gain obtained from selecting the segregating parents early in the breeding cycle (at F1 or F2 stages) was substantially higher than selecting at later stages even though prediction accuracy was moderate. Increasing the number of F1 intercross (F1i) families and keeping the total number of progeny of F1i families constant, we observed a decrease in genetic gain and increase in genetic diversity, whereas increasing the number of progeny per F1i family while keeping a constant number of F1i families increased the rate of genetic gain and had higher genetic diversity loss per unit of time. Adding 50 F2 family phenotypes to the training population increased the accuracy of genomic breeding values (GEBVs) and genetic gain per year and decreased the rate of genetic diversity loss. Genetic diversity could be preserved by applying a strategy that restricted both the percentage of alleles fixed and the average relationship of the group of selected parents to preserve long-term genetic improvement in the pulse breeding program.

A Preliminary Investigation on the Functional Validation and Interactions of PoWOX Genes in Peony (Paeonia ostii)

As a woody plant, peony (Paeonia suffruticosa) has a long growth cycle and inefficient traditional breeding techniques. There is an urgent need in peony molecular breeding to establish an efficient and stable in vitro regeneration and genetic transformation system, in order to overcome the recalcitrant characteristics of peony regeneration and shorten the breeding cycle. The development of plant somatic embryos is an important way to establish an efficient and stable in vitro regeneration and genetic transformation system. Plant-specific WUSCHEL-related homeobox (WOX) family transcription factors play important roles in plant development, from embryogenesis to lateral organ development. Therefore, in this research, four PoWOX genes of “Fengdan” (Paeonia ostii) were cloned from the peony genome and transcriptome data of preliminary peony somatic embryos. The sequence characteristics and evolutionary relationships of the PoWOX genes were analyzed. It was demonstrated that the four PoWOX genes, named PoWOX1, PoWOX4, PoWOX11, and PoWOX13, belonged to three branches of the WOX gene family. Their expression patterns were analyzed at different stages of development and in different tissues of peony seedlings. The expression localization of the PoWOX genes was determined to be the nucleus via subcellular localization assay. Finally, the interaction protein of the PoWOX genes was identified via yeast two-hybrid assay combined with bimolecular fluorescence complementation assay. It was shown that PoWOX1 and PoWOX13 proteins could form homodimers by themselves, and PoWOX11 interacted with PoWOX1 and PoWOX13 to form heterodimers. Peony stem cell activity may be regulated from PoWOX1 and PoWOX13 by forming dimers and moving to peony stem cells through plasmodesmata. Additionally, PoWOX11–PoWOX1 and PoWOX11–PoWOX13 may play important regulatory functions in promoting the proliferation of stem cells and maintaining the homeostasis of stem cells in the SAM of peony stems. Exploring the critical genes and regulatory factors in the development of the peony somatic embryo is beneficial not only to understand the molecular and regulatory mechanisms of peony somatic embryo development but also to achieve directed breeding and improvements in efficiency through genetic engineering breeding technology to accelerate the fundamental process of molecular breeding in peony.

A novel brain-penetrant oral UGT8 inhibitor decreases in vivo galactosphingolipid biosynthesis in murine Krabbe disease

Krabbe disease is a rare, inherited neurodegenerative disease due to impaired lysosomal β-galactosylceramidase (GALC) activity and formation of neurotoxic β-galactosylsphingosine (‘psychosine’). We investigated substrate reduction therapy with a novel brain-penetrant inhibitor of galactosylceramide biosynthesis, RA 5557, in twitcher mice that lack GALC activity and model Krabbe disease. This thienopyridine derivative selectively inhibits uridine diphosphate-galactose glycosyltransferase 8 (UGT8), the final step in the generation of galactosylceramides which are precursors of sulphatide and, in the pathological lysosome, the immediate source of psychosine. Administration of RA 5557, reduced pathologically elevated psychosine concentrations (72–86%) in the midbrain and cerebral cortex in twitcher mice: the inhibitor decreased galactosylceramides by about 70% in midbrain and cerebral cortex in mutant and wild type animals. Exposure to the inhibitor significantly decreased several characteristic inflammatory response markers without causing apparent toxicity to myelin-producing cells in wild type and mutant mice; transcript abundance of oligodendrocyte markers MBP (myelin basic protein) and murine UGT8 was unchanged. Administration of the inhibitor before conception and during several breeding cycles to mice did not impair fertility and gave rise to healthy offspring. Nevertheless, given the unchanged lifespan, it appears that GALC has critical functions in the nervous system beyond the hydrolysis of galactosylceramide and galactosylsphingosine. Our findings support further therapeutic exploration of orally active UGT8 inhibitors in Krabbe disease and related galactosphingolipid disorders. The potent thienopyridine derivative with effective target engagement here studied appears to have an acceptable safety profile in vivo; judicious dose optimization will be needed to ensure efficacious clinical translation.

The ‘Minibulk’ system for advancing winter cereal breeding populations

AbstractConventional selected‐bulk breeding is a low cost means of advancing populations but requires years of selection in the field to generate fixed lines. Doubled haploid (DH) methods produce fixed lines quickly but without selection and at high cost. The ‘Minibulk’ system was developed to combine the speed of DHs with the population size and crossover opportunities of selected‐bulk breeding. Breeding populations of winter wheat (Triticum aestivum L.) were vernalized and advanced at high density in the greenhouse from the F2 to the F4 generation. F4 populations underwent visual selection in the field, and derived lines were genotyped for variants at photoperiod and vernalization alleles and across the genome using genotyping‐by‐sequencing. The number of crossover events and parental genome contributions were determined for recombinant inbred lines (RILs) within populations and among RILs across populations. During vernalization, seeds in all populations germinated and underwent vegetative growth, forming a dense seed mat that was transplanted directly into greenhouse pots. A 22‐h photoperiod accelerated development, and many populations reached physiological maturity as soon as five weeks after transplanting. Increasing the number of seeds planted from 300 in the F2 to 500 in the F3 increased the number of fertile spikes produced, thereby maintaining a larger population size. The number of crossovers detected differed significantly between populations and chromosomes, while the number of crossovers detected in each population was related to marker density. Adoption of the minibulk system by winter cereal breeding programs can lead to significant cost savings and acceleration of the breeding cycle.

Cultivation and breeding of industrial Cannabis sativa

Cannabis sativa,with a long history of cultivation, is a traditional industrial crop widely used for food, textiles, and me-dicine. This study discussed industrial C. sativa and medicinal C. sativa. According to the characteristics of management policies of C. sativa in different periods, we divided the development stages of C. sativa into three stages and analyzed the changes in breeding and cultivation goals under the influence of policies. Meanwhile, a comprehensive analysis was carried out based on the breeding conditions of industrial C. sativa in China. Because of the vast territory of China, the differences in agricultural planting environment, economic development, and social development in the southern and northern areas result in different used parts of C. sativa. To be speci-fic, flowers and leaves are used in Yunnan, fiber in Heilongjiang, and seeds in Shanxi. The breeding of C. sativa varieties highlights fiber, seeds, or both of them. As the value of cannabidiol is explored, medicinal C. sativa has been approved in recent years. Based on the cultivation characteristics and value of industrial C. sativa, it is proposed that industrial C. sativa has a broad application prospect as an important industrial crop, and the existing products contain almost no tetrahydrocannabinol. The cultivation of C. sativa should be rationally guided to promote the development of the C. sativa industry. Moreover, it is recommended to actively apply advanced breeding techniques such as molecular breeding to overcome the problems of the uncertainty of the existing induced breeding and the excessively long hybrid breeding cycle, and develop high value-added applications such as medicinal products of C. sativa to enhance the exploitation of the economic value of C. sativa.

R12 Metamorphosis Theory In Creation Of The Universe With Dyniviti Pradigm And Economic Covid Era

The purpose of this study is to analyze the creation of the universe with the Dynic Paradigm according to the R12 Metamorphosis Reproduction (Metamorep) Theory in the 6 stages of the Covid economic era. The theory of R12 metamorphosis is based on the formula R12 and the Metamorphosis pattern. R12 is the Roikhan-12 formula that develops the Initial Edge Concept. The Metamorphosis Pattern is found in the changes in the Butterfly from the beginning. The Dynic Paradigm refers to the content of the scriptures according to truth and facts. This research was conducted in a desk study by collecting sources from scriptures, journals, books, and electronic media. The methodology used is Reflective Qualitative. The method used is metaphor and similarity. The result obtained is the Theory R12 Metamorphosis in the creation of the universe consists of 6 stages. This stage is a combination of the butterfly life cycle plus the creature's breeding cycle. It starts with 1 dot like an egg which contains high-density matter. Then there was a separation which was called the Early Edge Concept. Similar to this concept is the meaning of the Quran Surah Hid 11.114 which is interpreted as a separation from 1 solid dot into 2 parts, namely the edge of the universe's matter has 2 parts, and at the beginning of the universe's matter, there is 1 part in the caterpillar metaphor. Followed by the transformation into a Nebula with smoke covering the galaxy with the metaphor of a cocoon with the reflexivity of the universe praying. The last stage of Metamorphosis is the Butterfly which is represented in the form of the universe starting to develop at the beginning of its perfection. Two additional stages are before the reproductive period with the maturity level of the young universe. The last is the reproduction phase of the universe with a more mature maturity. The Dynic Paradigm is a solution for the development of the theory of the creation of the universe that combines existing theories with the contents of the holy book of the Covid economic era.

Double Haploids for Vegetable Crop Improvement: A Review

Vegetables are the richest source of vitamins and minerals and play a major role in nutritional security. The primary objective of vegetable breeding is enhancing production and productivity. Breeders use various conventional and non-conventional breeding approaches for genetic advance. Recent advances in biotechnology helps to enhance the efficiency and shorten the time required to achieve the fixed goals in a breeding program, as well as to address the economic and ecological goals. Among these, haploid (H) and doubled haploid (DH) production through gametic embryogenesis has long been recognized as a valuable tool to help crop improvement. Haploid plants are the sporophytes with a gametophytic chromosome number and doubled haploids (DH) are haploids that have undergone chromosome duplication. Haploids and double haploids occur spontaneously in nature. Haploids can also be induced artificially by various techniques such as wide hybridization, pollination with irradiated pollens androgenesis, gynogenesis and finally further chromosome doubling results in double haploids. Production of double haploids in vegetables will shorten the breeding cycle and also DH technology is useful in reverse breeding, CMS line production, gene stacking and various other genetic studies.

Genomic Selection: A Tool for Accelerating the Efficiency of Molecular Breeding for Development of Climate-Resilient Crops.

Since the inception of the theory and conceptual framework of genomic selection (GS), extensive research has been done on evaluating its efficiency for utilization in crop improvement. Though, the marker-assisted selection has proven its potential for improvement of qualitative traits controlled by one to few genes with large effects. Its role in improving quantitative traits controlled by several genes with small effects is limited. In this regard, GS that utilizes genomic-estimated breeding values of individuals obtained from genome-wide markers to choose candidates for the next breeding cycle is a powerful approach to improve quantitative traits. In the last two decades, GS has been widely adopted in animal breeding programs globally because of its potential to improve selection accuracy, minimize phenotyping, reduce cycle time, and increase genetic gains. In addition, given the promising initial evaluation outcomes of GS for the improvement of yield, biotic and abiotic stress tolerance, and quality in cereal crops like wheat, maize, and rice, prospects of integrating it in breeding crops are also being explored. Improved statistical models that leverage the genomic information to increase the prediction accuracies are critical for the effectiveness of GS-enabled breeding programs. Study on genetic architecture under drought and heat stress helps in developing production markers that can significantly accelerate the development of stress-resilient crop varieties through GS. This review focuses on the transition from traditional selection methods to GS, underlying statistical methods and tools used for this purpose, current status of GS studies in crop plants, and perspectives for its successful implementation in the development of climate-resilient crops.

Intercross: An Android app for plant breeding and genetics cross management

AbstractPlant breeding is fundamentally comprised of three cyclic activities: (a) intermating lines to generate novel allelic combinations, (b) evaluating the newly created lines in diverse environments, and (c) selecting superior individuals to be used as parents in the next breeding cycle. While digital technologies and tools are commonly utilized for the latter two stages, many plant research programs still rely on manual annotation and paper tags to track the crosses that constitute the basis of a plant breeding program. This presence of analog data is a crack in the foundation of a digital breeding ecosystem and a significant occasion for errors to be introduced that will propagate through the entire breeding process. However, implementing digital cross tracking into breeding programs is difficult due to the nonstandardized workflows that different breeders have adopted. Intercross, an open‐source Android app, aims to provide scientists with a robust and simple solution for planning, tracking, and managing the crosses being made each season and aims to serve as the primary tool to digitize crossing data for breeding programs. The simplicity and flexibility of Intercross allows rapid and broad adoption by diverse breeding programs and will solidify the concepts of a digital breeding ecosystem.

Empirical assessment of a genomic breeding strategy in perennial ryegrass

In genomic selection (GS) DNA markers and trait data are integrated in a model that then predicts genomic-estimated breeding values (GEBV’s) for individuals using DNA marker information alone, improving breeding efficiency. We assessed a genomic breeding strategy (APWFGS) for improving dry matter yield (DMY) in perennial ryegrass. In APWFGS the best-performing half-sibling families (HS) are identified using phenotypic data and GS is used to select the best individuals within those HS. Four selections were made from three breeding populations: Base (random sample of plants from all HS), HSP (random sample from the six phenotypically-best HS), APWFGS and APWFGS-L (top or bottom 5% of plants, respectively, selected by GEBV from the six HS). Selected plants were polycrossed, creating 12 experimental synthetics that were evaluated as sown rows for DMY (n=7 harvests) in field trials at two locations over 18 months. In each population, mean DMY across locations and harvests showed a trend of APWFGS> HSP>Base. Averaged across all populations, APWFGS increased DMY by 43% (P<0.05) compared to Base, more than twice the level of improvement achieved with conventional HSP. Our results show the APWFGS breeding approach can substantially improve selection response for a genetically complex trait from a single breeding cycle.

Corneal Changes and Strategies to Improve Survival of Hypomorphic Collagen VII-Deficient Mice for the Study of Ocular Dystrophic Epidermolysis Bullosa.

Ophthalmic study of collagen CVII hypomorphic mice is uniquely challenging due to the strain's published survival rate to weaning of 24%. Because chronic ocular fibrosis requires time to develop, optimizing the survival rate is of critical importance. In this study, standard husbandry practices were enhanced by the addition of sterilized diet and drug delivery gels, acidified water, irradiated food pellets, cellulose fiber bedding, minimal handling, removal of siblings within 2-3 wk from birth, and a preferred housing location. Survival rates per breeding cycle, sex, weight, and cause of early euthanasia were recorded and analyzed over 43 mo. Overall, 49% of mice survived to weaning and 76% of weaned mice survived to 20 wk of age. Corneal opacities were seen in 65% of mice by 20 wk, but only 10% of eyes showed the sustained opacification that was indicative of fibrosis. Corneal opacities occurred at the same rate as in humans with epidermolysis bullosa. 66% of the mice showed weight loss at 11 wk. Males required early euthanasia 4 times more often than did females. Euthanasia was required for urinary obstruction due to penile prolapse in 88% of males. With our enhanced care protocol, hypomorphic mice in our colony survived at twice the published rate. With this revised husbandry standard, experiments planned with termination endpoints of 14 wk for males and 17 wk for females are more likely to reach completion.

Progeny selection for enhanced forest growth alters soil communities and processes

AbstractGenetic enhancement of tree species is integral to global forest management practices with mass propagation of enhanced plant material being used to reforest whole landscapes. It is unclear, however, how genetic enhancement of basic traits such as tree growth may influence the function of life supporting soil ecosystems. We studied the potential cascading effects of genetic increases in growth of Norway spruce (Picea abies) on a range of soil chemical and biological properties. Because this species is a prime candidate for the genetic enhancement of boreal forest landscapes and it has been introduced around the world, its impacts on soil microbiomes are likely of importance both locally and globally. In a 40‐year common garden, we assessed how genetic increases in growth generated through controlled crossing of high‐quality “plus” trees from across the central boreal zone of Sweden influenced a range of soil properties beneath the canopies. Properties included pH, carbon, nitrogen, nitrate, ammonium, phosphate, respiration rate, and the composition of microbial communities assessed via phospholipid fatty acids (PLFAs). We found that Norway spruce family significantly affected each of the seven chemical properties assessed, with differences of up to 140% among families, and that three of the seven were significantly correlated with mean family growth rate. We also found that fungal PLFAs varied significantly across Norway spruce families, but these differences were not strongly related to mean family growth rate. This study, representing just one cycle of selective breeding, suggests that genetic increases in tree growth rates may also be inadvertently altering soil communities and ecosystem services. Such alterations across forest landscapes may have unexpected implications for the function of forest ecosystems (i.e., nutrient cycling) as well as processes of global significance (i.e., carbon sequestration).

Microclimate-driven trends in spring-emergence phenology in a temperate reptile (Vipera berus): Evidence for a potential "climate trap"?

Climate change can not only increase the exposure of organisms to higher temperatures but can also drive phenological shifts that alter their susceptibility to conditions at the onset of breeding cycles. Organisms rely on climatic cues to time annual life cycle events, but the extent to which climate change has altered cue reliability remains unclear. Here, we examined the risk of a “climate trap”—a climatically driven desynchronization of the cues that determine life cycle events and fitness later in the season in a temperate reptile, the European adder (Vipera berus). During the winter, adders hibernate underground, buffered against subzero temperatures, and re‐emerge in the spring to reproduce. We derived annual spring‐emergence trends between 1983 and 2017 from historical observations in Cornwall, UK, and related these trends to the microclimatic conditions that adders experienced. Using a mechanistic microclimate model, we computed below‐ and near‐ground temperatures to derive accumulated degree‐hour and absolute temperature thresholds that predicted annual spring‐emergence timing. Trends in annual‐emergence timing and subsequent exposure to ground frost were then quantified. We found that adders have advanced their phenology toward earlier emergence. Earlier emergence was associated with increased exposure to ground frost and, contradicting the expected effects of macroclimate warming, increased post‐emergence exposure to ground frost at some locations. The susceptibility of adders to this “climate trap” was related to the rate at which frost risk diminishes relative to advancement in phenology, which depends on the seasonality of climate. We emphasize the need to consider exposure to changing microclimatic conditions when forecasting biological impacts of climate change.

Length-Weight Relationship and Condition Factor of African Mud Catfish (Clarias gariepinus (Burchell 1822) and Tilapia (Oreochromis nilotica Linnaeus 1758) in Orashi River of Ogba/Egbema/Ndoni Lga of Rivers State, Nigeria

Length-weight relationship and condition factor are important in fishery assessment studies since it provide information about the growth of the fish, its general wellbeing and fitness in aquatic habitat. LWRs for 2 fish species –Clarias gariepinus (Burchell 1822) and Oreochromis nilotica (Linnaeus 1758) collected from Orashi River were established and their growth condition was evaluated. The study was carried out from September 2019 to August 2020. The biometric measurement (length/weight) shows that the weight of the fish increased in proportion to its length as indicated by the slope (b) of the relationship. The mean value shows strong relationship because coefficient of determination (R2) is >0.5 and range from 0.795-0.985. Higher values of both length and weight were recorded for Catfish over Tilapia. The results indicated that almost all the fish sampled exhibited a positive allometric growth and trended to grow bigger. All relationship were statistically significant (p=0.05). The mean Fulton’s condition factor (K) of the fish range from Catfish (1.24-1.80) and Tilapia (1.5-3.7) in the 5 stations sampled. The result showed that Tilapia had a high mean range and therefore was in better conditions than the Catfish. This gives information on the food supply, timing and duration of breeding cycle. The indices may also be used in the general assessment of the “well being” of a fish [1]. Multiple comparison tests using Turkey Kramer showed that the condition factor of Catfish from Okwuzi (station 1) was significantly different from that of Ndoni and Omoku but Ebocha and Obrikom was not significantly different from each other. With regards to seasonal variation, dry season recorded higher values than rainy season.

Adoption of improved cassava varieties by processors is linked to processing characteristics and products biophysical attributes

Evidence from community cassava processors on product quality traits that influence variety adoption was combined with laboratory methods to identify potential predictors of quality traits of new varieties. The study revealed that high product yield, high starch content, high solubility index (SI), high peak viscosity (PV), low setback viscosity, and delayed root color change (delayed postharvest physiological deterioration) are possible laboratory indicators that could be used as proxies for predicting product quality and variety adoption decisions of cassava processors. Fufu exhibited higher swelling power, SI, and PV than gari from the same varieties. Processors preferred quality characteristics are difficult to measure for several hundreds of new germplasms in the early stages of the breeding cycle. The information presented may be helpful during the breeding of new, improved varieties by using the physical and chemical properties of the roots that predict processors’ preferred quality traits. Practical applications The study identified laboratory parameters that could be used as predictors of processors-preferred traits in new breeding lines with a higher possibility of adoption by processors to make commercial success products.

Effect of Pot Size and Transplanting Date on Tuber Production Using Micro-Tubers of White Yam

Low multiplication ratio, long growth and development duration contribute to the long conventional breeding cycle of yams. Moreover, little is known about the effect of pot size and transplanting date on the yield of introduced semi-autotrophic hydroponics (SAH) derived micro-tubers of white yam (Dioscrearotundata Poir). This study was carried out to evaluate the effect of pot size and transplanting date on tuber production of introduced SAH micro-tuber derived white yam var TDr9719177 in shed-house conditions. The SAH materials were introduced from the International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria. The trial involved two factors including two different pot sizes (38.5×28.5cm and 29.5×23.0cm) and two transplanting dates (September, 2020 and October, 2020). The results showed that micro-tubers grown in the big pot (38.5×28.5cm) significantly out yielded those established in the small pot (29.5×23.0cm). Transplanting in September produced heavier fresh tubers per plant (123.4g)and fresh tuber weight per tuber (88.8g) than transplanting in October, which had 17.4g and 14.1g, respectively. The mean difference of fresh tuber weight per plant between the transplanting pots was 68.4%, and between the transplanting dates was 85.9%. The mean difference of weight per tuber between the transplanting pots was 74.2%, and between the transplanting dates was 84.1%. The results suggested the relevance of early transplanting of healthy seedlings from SAH derived micro-tubers that could be exploited for deployment and promotion to seed yam producers for increased yam productivity. It also depicted the relevance of transplanting SAH micro-tubers in big container that promotes higher tuber production that could be exploited for the rapid multiplication of early generation seeds in yam breeding.

Effects of non-aversive versus tail-lift handling on breeding productivity in a C57BL/6J mouse colony.

Non-aversive handling is a well-documented refinement measure for improving rodent welfare. Because maternal stress is related to reduced productivity, we hypothesized that welfare benefits associated with non-aversive handling would translate to higher production and fewer litters lost in a laboratory mouse breeding colony. We performed a randomized controlled trial to examine the effects of a standard method of handling (tail-lift with forceps) versus non-aversive handling with transfer tunnels ('tunnel-handled') on breeding performance in 59 C57BL/6J mouse pairs. Intervention assignments could not be concealed from technicians, but were concealed from assessors and data analyst. An operationally significant effect of tunnel-handling (large enough differences to warrant programmatic change) was defined before study initiation as a 5% increase in productivity, or one extra pup over the reproductive lifetime of each pair. Pairs were randomly allocated to handling intervention and cage rack location, and monitored over an entire 6-month breeding cycle. For each group, we measured number of pups born and weaned, and number of entire litters lost prior to weaning. Differences between transfer methods were estimated by two-level hierarchical mixed models adjusted for parental effects and parity. Compared to tail-lift mice, tunnel-handled mice averaged one extra pup per pair born (+1.0; 95% CI 0.9, 1.1; P = 0.41) and weaned (+1.1, 95% CI 0.9, 1.2; P = 0.33). More tunnel-handled pairs successfully weaned all litters produced (13/29 pairs, 45% vs 4/30 pairs, 13%; P = 0.015), averaged fewer litter losses prior to weaning (11/29 pairs [38%] vs 26/30 pairs [87%]; P <0.001), and had a 20% lower risk of recurrent litter loss. The increase in numbers of pups produced and weaned with tunnel handling met threshold requirement for operational significance. These data and projected cost savings persuaded management to incorporate tunnel handling as standard of care across the institution. These data also suggest that overlooked husbandry practices such as cage transfer may be major confounders in studies of mouse models.

Molecular markers to devise predictive models for juvenile selection in Hevea rubber

AbstractNatural rubber is extracted from the Hevea tree, through shaving the bark. As a major raw material source for many industries especially the tyre sector, Hevea rubber clones are intensively cultivated in the tropics. The world production of Hevea rubber is almost 13.64 million metric tonnes, and the productivity is around 1200 kg ha−1. However, the field production achieved so far is still well below the theoretical yield estimated (7000–12,000 kg ha−1). Even though this is a calculated estimate, efforts can be kept live to achieve this target, because Hevea rubber is being increasingly cultivated under several suboptimal environments after the 1980s. In this era of climate change, newer biotic and abiotic stresses encounter Hevea rubber culture that demands new clones at definite intervals. Hence, like any other species, Hevea rubber breeding is a continuous process in quest of new clones achieved through exploiting new sources of genetic variation. Hevea rubber breeding is to produce high‐yielding clones with good timber value. First priority is to explore and exploit genetic variation in clones, half‐sib, full‐sib and illegitimate (open‐pollinated) seedlings, where dry rubber yield and wood volume are the target traits. Next is to maximize genetic gains per unit time, through understanding juvenile–mature correlations and to practice selection of high‐yielding genotypes at the juvenile stage. Hevea rubber had a long breeding cycle of 33 years but could be reduced to 17 years after culling non‐essential steps of deriving clones. However, this could be reduced to 10 years, if a DNA marker‐assisted selection system is applied to seedlings. This system must also ensure significant juvenile–mature correlations on yield. This is a formidable task because under given circumstances, such a correlation is almost absent. However, this can be turned into a reality through employing yield‐related DNA markers with genomic selection (GS). The impact of DNA markers linked with REF, SRPP, acetyl‐CoA acetyltransferase, HMGS, HMGR and JAZ need to be specifically evaluated. GS that aims to improve quantitative traits by using genome‐wide marker data without requiring identification of markers associated with quantitative trait loci (QTLs) of interest can be used in Hevea also. Subsequently, by a predictive model, genomic estimated breeding values (GEBVs) can be calculated for untested individuals from a ‘testing population’. GS captures the total additive genetic variance with genome‐wide marker coverage and effect estimates. Therefore, selection of an individual without phenotypic data can be performed based on the individual's predicted breeding value. This review makes an assessment of the molecular markers in Hevea rubber and aims to streamline an efficient selection system to be applied onto seedlings through GS that owes a significant correlation with the mature phase.

Prospectus of Genomic Selection and Phenomics in Cereal, Legume and Oilseed Breeding Programs

The last decade witnessed an unprecedented increase in the adoption of genomic selection (GS) and phenomics tools in plant breeding programs, especially in major cereal crops. GS has demonstrated the potential for selecting superior genotypes with high precision and accelerating the breeding cycle. Phenomics is a rapidly advancing domain to alleviate phenotyping bottlenecks and explores new large-scale phenotyping and data acquisition methods. In this review, we discuss the lesson learned from GS and phenomics in six self-pollinated crops, primarily focusing on rice, wheat, soybean, common bean, chickpea, and groundnut, and their implementation schemes are discussed after assessing their impact in the breeding programs. Here, the status of the adoption of genomics and phenomics is provided for those crops, with a complete GS overview. GS’s progress until 2020 is discussed in detail, and relevant information and links to the source codes are provided for implementing this technology into plant breeding programs, with most of the examples from wheat breeding programs. Detailed information about various phenotyping tools is provided to strengthen the field of phenomics for a plant breeder in the coming years. Finally, we highlight the benefits of merging genomic selection, phenomics, and machine and deep learning that have resulted in extraordinary results during recent years in wheat, rice, and soybean. Hence, there is a potential for adopting these technologies into crops like the common bean, chickpea, and groundnut. The adoption of phenomics and GS into different breeding programs will accelerate genetic gain that would create an impact on food security, realizing the need to feed an ever-growing population.