Actual Breeding Research Articles

Study of the gene pool of the winter rye Secale cereale L. of the Republic of Belarus using microsatellite markers

In this work, the genetic diversity of the modern gene pool of the winter rye (S. cereal L.) of the Republic of Belarus from 20 actual breeding samples was investigated using 15 microsatellite (SSR) markers to develop divergent crossing combinations in breeding for heterosis. It was shown that the formed set of SSR markers is highly effective – the informational content index (PIC) varied from 0.50 to 0.83 and averaged 0.72. The most effective microsatellite markers (SCM28, SCM43, SCM101 and SCM102) were identified and can be successfully used to study the genetic diversity of rye. It has been established that the modern gene pool of the winter rye of the Republic of Belarus is generally characterized by fairly wide genetic diversity (interpopulation variability) – all collection samples are characterized by a unique allelic composition of the studied microsatellite loci. Based on investigation results, a hierarchical clustering dendrogram was constructed, which made it possible to determine the most genetically divergent combinations of crosses. The information obtained can be used for the development of an effective scheme allowing to develop new varieties and hybrids in the practical breeding of rye for heterosis.

Correcting parentage relationships in the endangered California Condor: Improving mean kinship estimates for conservation management

Abstract Maintaining the existing biodiversity of endangered species is a goal of conservation management programs, and a major component of many collaborative efforts undertaken by zoos, field biologists, and conservation scientists. Over the past 3 decades, the San Diego Zoo has performed long-term genetic studies in support of the recovery program for the critically endangered California Condor (Gymnogyps californianus). This work has included sex determination of hatchlings and parentage confirmation using microsatellite genotyping. This paper describes the genetic work associated with the California Condor recovery program, which aims to provide a highly accurate pedigree for making informed captive pairing and release recommendations. Initial genotyping began after reintroduced California Condors started reproducing, and the focus was on birds hatched from their wild-laid eggs. However, genetic analysis showed discrepancies relative to behavioral observations of wild birds and led to the species-wide testing of all available samples. This genetic study has resolved instances of individual misidentifications and parental misassignments, verified the first cases of extra-pair paternity in this species, identified parentage where chicks were observed being raised by trios, and found 2 apparent de novo mutations in the captive condor population. Correcting the California Condor pedigree according to genetic parental analysis has produced more accurate estimates of mean kinship values among living birds, ranking potential breeders according to their actual breeding value and helping managers to make informed decisions about captive pairing and release of condors in the wild.

The look ahead trace back optimizer for genomic selection under transparent and opaque simulators

Recent advances in genomic selection (GS) have demonstrated the importance of not only the accuracy of genomic prediction but also the intelligence of selection strategies. The look ahead selection algorithm, for example, has been found to significantly outperform the widely used truncation selection approach in terms of genetic gain, thanks to its strategy of selecting breeding parents that may not necessarily be elite themselves but have the best chance of producing elite progeny in the future. This paper presents the look ahead trace back algorithm as a new variant of the look ahead approach, which introduces several improvements to further accelerate genetic gain especially under imperfect genomic prediction. Perhaps an even more significant contribution of this paper is the design of opaque simulators for evaluating the performance of GS algorithms. These simulators are partially observable, explicitly capture both additive and non-additive genetic effects, and simulate uncertain recombination events more realistically. In contrast, most existing GS simulation settings are transparent, either explicitly or implicitly allowing the GS algorithm to exploit certain critical information that may not be possible in actual breeding programs. Comprehensive computational experiments were carried out using a maize data set to compare a variety of GS algorithms under four simulators with different levels of opacity. These results reveal how differently a same GS algorithm would interact with different simulators, suggesting the need for continued research in the design of more realistic simulators. As long as GS algorithms continue to be trained in silico rather than in planta, the best way to avoid disappointing discrepancy between their simulated and actual performances may be to make the simulator as akin to the complex and opaque nature as possible.

Three-dimensional motion of the patella in French bulldogs with and without medial patellar luxation

BackgroundFrench bulldogs exhibit significantly larger femoral external rotation and abduction than other breeds. We were curious as to whether this peculiar leg kinematic affects patellar motion and/or might induce medial patellar subluxation (MPSL) or medial patellar permanent luxation (MPPL). We hypothesized that the more abducted leg posture during stance causes an unusual medial pull direction of the rectus femoris muscle during stance, and that this may facilitate the occurrence of MPSL or even MPPL during locomotion. To test our hypothesis, we analyzed existing stifle-joint X-ray-sequences collected during the treadmill walk and trot of seven adult female French bulldogs. We estimated 3D-patellar kinematics using Scientific Rotoscoping.ResultsThe three-dimensional motion of the patella comprises rotations and translations. From the seven dogs analyzed, three exhibited MPSL and one MPPL during the gait cycle. Medial patellar luxation (MPL) occurred mostly around toe-off in both gaits studied.Patellar position was generally not gait-related at the analyzed timepoints. In dogs with MPL, the patella was placed significantly more distally (p = 0.037) at touch-down (TD) and at midswing (p = 0.024), and significantly more medial at midswing (p = 0.045) compared to dogs without MPL.ConclusionsMedial patellar luxation seems to be the consequence of the far from parasagittal position of the stifle joint during stance due to a broad trunk, and a wide pelvis. This peculiar leg orientation leads to a medial sideway pull caused by the rectus femoris muscle and the quadriceps femoris and may initiate plastic deformation of the growing femur and tibia. Thus, a way to avoid MPL could be to control breeding by selecting dogs with lean bodies and narrow pelvis. Actual breeding control programs based on the orthopedic examination are susceptible to errors. Systematic errors arise from the fact that the grading system is highly dependent on the dog’s condition and the veterinarians’ ability to perform the palpation on the stifle. Based on our results, the position of the patella at TD, or even perhaps during stand might offer a possibility of an objective radioscopic diagnostic of the MPL.

Cumulative dairy cow genetic change from selection and crossbreeding over the last 2 decades in New Zealand closely aligns to model-based predictions published in 2000

A deterministic model was developed in 1998 to evaluate the concurrent effects of selection and crossbreeding on the rate of genetic gain and increases in productivity of New Zealand dairy cattle over the ensuing 25-yr period. The predictions of today's breed composition of the national dairy herd and genetic trends for body weight and lactation yields of milk, fat, and protein are compared with today's actual values. Selection was assumed to use an index that included live weight and lactation yields of milk, fat, and protein. Mating strategies involving the Holstein-Friesian (F), Jersey (J), and Ayrshire (A) breeds were evaluated. Effects of heterosis and age were included to calculate phenotypic live weight and yields of milk, fat, and protein per cow. At the time the model was developed, New Zealand had an across-breed evaluation system, but only straightbred bulls were used after progeny testing based on records of straightbred and crossbred daughters. The model predicted that if crossbred cows and bulls could be considered as bull parents, faster rates of genetic gain may result because of increased selection intensities in the cow to breed bull selection pathway. This scenario transpired, and the best bulls and cows for farm profit were used regardless of breed. Under that mating strategy for the 2018 birthyear, the model predicted the national breed composition would be 11% F, 34% J, 52% F×J, and 2% A; the actual breed composition was 36% F, 9% J, 53% F×J, and 1% A. The model-predicted annual genetic gains would be 16.7 L of milk, 1.2 kg of fat, 1.5 kg of protein, and −0.7 kg of body weight; the realized annual improvements were 13.6 L of milk, 1.31 kg of fat, 1.17 kg of protein, and −0.36 kg of body weight. Predicted long-term responses to selection can closely mirror realized improvements, confirming the value of modeling to inform animal breeding decision-making.

Pollution characteristics of livestock faeces and the key driver of the spread of antibiotic resistance genes

The increasing prevalence of antibiotic resistance genes (ARGs) in livestock and poultry faeces has attracted considerable amounts of attention. However, in the actual breeding environment, the key driver of the spread of ARGs and which bacteria are involved remain unclear. This study investigated 19 antibiotics and 4 heavy metals in 147 animal faeces. The results showed that piglet faeces exhibited the highest levels of antibiotics and heavy metals. Twelve ARGs, 4 mobile genetic elements (MGEs) and bacterial communities of piglet faeces from 6 pig farms were further assessed to determine the key driver and relevant mechanism of the spread of ARGs. Sulphonamides (SAs) explained 36.5% of the variance (P < 0.05) of the bacterial community and were significantly related to 8 genes (P < 0.01), indicating that SAs dominated the spread of ARGs and should be tightly supervised. Structural equation modelling (SEM) indicated that SAs increased the abundance of ARGs via two pathways: horizontal transfer of ARGs (involving 10 genera) and vertical transfer of ARGs (involving 26 genera). These results improve our understanding of the potential hosts involved in the spread of ARGs, suggesting that monitoring of the above potential hosts is also important in animal feeding practice.

Historical Changes and Description of the Current Hungarian Hucul Horse Population.

Simple SummaryOriginally, the Hucul horse breed was bred in the northeastern parts of the forested Carpathians. Only a few animals survived the Second World War and the regeneration of the breed started in those times. The aim of the current work was to give an overview of this rescue work from gene conservation point of view with the evaluation of the population changes within this few decades-long time interval. The pedigree quality, gene origin, inbreeding and status of stallion lines and mare families were evaluated. The main finding of the study was that inbreeding in the recent years was successfully limited and current inbreeding levels are the reason of previous gene fixations. Due to the increased number of mare families, genetic variability also increased. However, the proper management of the stallion utilization is important to prevent the future increasing of the inbreeding level of the Hucul breed.Gene conservation and management of small populations requires proper knowledge of the background and history of the breed. The aim of the study was the evaluation of population structure and changes of the Hungarian Hucul horse population. Population changes were described for the actual breeding stock as well as for groups of 10-year epochs reflecting major periods of change in the breed. Pedigree data of the registered population were analyzed using Endog and GRain software. The average value of equivalent complete generations was above nine for the actual breeding population. The longest generation interval was the sire-to-daughter pathway. The fe/f ratio had smaller changes than fa/fe ratio across the population history. Inbreeding and average relatedness as well as ancestral coefficients had increased during history. Kalinowski’s decomposition of inbreeding showed that present inbreeding is smaller than it was done earlier during the last 20 years. Due to the continuous imports from other breeder countries, the genetic variability increased during the evaluated time periods.

Breeding range shift of the red-crowned crane (Grus japonensis) under climate change.

The red-crowned crane (Grus japonensis) is an endangered species listed by International Union for Conservation of Nature (IUCN) HARRIS J (2013). The largest population of this species is distributed mainly in China and Russia, which is called continental population SU L (2012)-Curt D (1996). This population is migratory, which migrates from its breeding range located in Northeast China and Southern Russia, to the wintering range in the south of China to spend the winter every year. The breeding range of this species is critical for red-crowned crane to survive and maintain its population. Previous studies showed the negative effects of habitat loss and degradation on the breeding area of red-crowned crane Ma Z (1998), Claire M (2019). Climate change may also threat the survival of this endangered species. Previous studies investigated the impacts of climate change on the breeding range or wintering range in China Wu (2012), [1]. However, no study was conducted to assess the potential impacts of climate change on the whole breeding range of this species. Here, we used bioclimatic niche modeling to predict the potential breeding range of red-crowned crane under current climate conditions and project onto future climate change scenarios. Our results show that the breeding range of the continental population of red-crowned crane will shift northward over this century and lose almost all of its current actual breeding range. The climate change will also change the country owning the largest portion of breeding range from China to Russia, suggesting that Russia should take more responsibility to preserve this endangered species in the future.

High Reproductive Success Despite Queuing - Socio-Sexual Development of Males in a Complex Social Environment.

The start of actual breeding in male social mammals can occur long after individuals attain sexual maturity. Mainly prevented from reproduction by older and dominant males, young males often queue until strong enough to compete for favorable social positions and, in this way, to obtain access to females. However, to what extent maturing males also apply tactics to reproduce before this time is largely unknown. Therefore, the aim of the present study was to elucidate male socio-sexual development from onset of sexual maturity through first mating success until the achievement of a stable social position in a complex social environment. For this purpose, guinea pigs were used as a model system and reproductive success of males living in large mixed-sex colonies was assessed during their first year of life. As a reference, males in a mixed-sex pair situation were examined. Pair-housed males reproduced for the first time around the onset of sexual maturity whereas colony-housed males did so much later in life and with a considerably higher variance. In colonies, reproductive success was significantly affected by dominance status. Dominance itself was age-dependent, with older males having significantly higher dominance ranks than younger males. Surprisingly, both younger and older colony-housed males attained substantial reproductive success of comparable amounts. Thus, younger males reproduced irrespective of queuing and already before reaching a high social status. This mating success of maturing males was most likely achieved via several reproductive tactics which were flexibly applied with the onset of sexual maturity. The period of socio-sexual development before a stable social position is established may, therefore, be a time during which male mammals use flexible behavioral tactics to achieve reproductive success more frequently than commonly is presumed. In addition, the findings strongly indicate that high behavioral plasticity exists well beyond sexual maturity.

Promising VNIISPK apple cultivars that are on state trials

More than 60 years of experience in creating apple cultivars that meet the high requirements of production, shows that breeders often do not have time to meet the increasing requirements for cultivars. This is due to the intensification of gardening and complication of fruit production technology, which imposes high requirements on breeders. The breeding strategy provides for the presence of more than 20 indicators in a new cultivar (the tree vigorousness, resistance to diseases, precocity, productivity, fruit quality, content of valuable vitamins, high marketability, etc.). In order for new cultivars to meet all the requirements, interdisciplinary teams of researchers are needed. In addition to breeders, researchers of many specialties should be included: geneticists, cytoembryologists, biochemists, physiologists, physiologists, agrotechnicians, etc. At VNIISPK, an average of 19 years is spent from hybridization to the advariant of a cultivar for state trials, and from hybridization to inclusion in the State Register it is spent 28 years. In this regard, it is necessary to reduce in time each stage of cultivar development: from the actual breeding process and primary study to the state trials. In this paper, brief economical and biological characteristics of 12 apple cultivars that are in the state trials and 2 zoned cultivars are given. From 12 to 29 years were spent to create the cultivars. A large period of time must still be spent before their inclusion in the State Register. In this regard, it is desirable to lay the gardens of a small production test of 20-40 trees of a new cultivar in each of the three repetitions together with the standard cultivars.

Apple breeding process duration and ways of its reduction

A careful 63-year-old work on apple breeding, resulting in the creation of 54 its varieties, included in the State Register of breeding achievements admitted for use, makes it possible to speak about the ways of reduction in the time of the actual breeding process and the subsequent stages of accelerating the introduction of new varieties into production. According to the experience of the Russian Research Institute of Fruit Crop Breeding, an average of 19 years is spent from hybridization to the adoption of a variety for State trials, and from hybridization to inclusion in the State Register it is spent 27 years. The requirements for new apple varieties are changing and becoming tougher to a large extent during this period. We off er the possibility of reducing the time to create a new variety by combining in time the actual breeding process and the primary variety study. For this purpose already during the selection and transfer of biannual seedlings to the breeding orchard it is necessary to multiply and include the best seedlings on morphological features with a culture of 5 points (no more than 1 seedling per thousand selected ones) in the primary study. In this case the actual breeding process is combined with the primary study. When transferring the variety to the state trial, it is necessary to lay orchards of a small production testing of 20-40 trees of a new variety in each of the three replications. The time of single breeders is a thing of the past. To create varieties that meet high requirements of production (convenient for cultivation, highly adapted to local conditions, with a certain shape of tree crowns, with the fruits of high commodity and consumer qualities), interdisciplinary teams are needed, which include not only breeders, but also pomologists, geneticists, cytoembryologists, biochemists, physiologists, phytopathologists, and agricultural technicians. Usually years, and sometimes decades are spent on the creation of well-coordinated teams of professionals of diff erent specialties, but only such teams are able to create varieties that meet all main requirements. At Russian Research Institute of Fruit Crop Breeding such a team consists of 22 people.

Determination of gentamicin C components in fish tissues through SPE-Hypercarb-HPLC-MS/MS

In this work, an HPLC/MS/MS method for determination of gentamicin C components in fish tissues was developed based on strong cation exchange solid-phase extraction (SPE) purification coupled with Hypercarb chromatographic column in separation mode. Sample was extracted using trichloroacetic acid aqueous solution containing EDTA. Ion-pairing reagents were not needed because of the “graphite polarity retention effect” of the Hypercarb chromatographic column. HPLC-MS/MS was performed in multiple reaction monitoring (MRM) mode for simultaneous qualitative and quantitative analyses (using matrix external standard) of gentamicin C components in fish tissues. Good linearity was obtained for the target analytes within the concentration range from 0.0100 to 0.500 mg/L. The limits of quantification (LOQ) of this method were 10.0, 20.0, and 20.0 μg/kg for C1, C1a, and sum of C2 + C2a, respectively. The average recoveries of gentamicin C components were 80.0%–110% when spiked at three levels with the blank carp (Cyprinus carpio) matrix, and the relative standard deviations (RSD) were all less than 15% (n = 6). In addition, for the features of simple operation, high sensitivity and good reproducibility, the proposed method has been successfully applied for detection of gentamicin residues in fish tissues during actual breeding.

A new subspecies of the black redstart – Phoenicurus ochruros murinus subsp. nov. from the Altai-Sayan Mountainous Country and the current breeding range of the black redstart

On the basis of literature and collection materials, as well as photographs with geo-referencing from various sources, the actual breeding range of the Black Redstart Phoenicurus ochruros (Gmelin, 1774) was compiled. For the Asian part of the range, a probabilistic model is constructed for the geographic distribution of the species by the maximum entropy method, which is used to refine the range in some of its regions. Based on the collection materials of the Zoological Museum of the Moscow State University (Moscow), Zoological Institute of the Russian Academy of Sciences (St. Petersburg) and Institute of Zoology of the Republic of Kazakhstan (Almaty), a comparison of the breeding plumages of adult male Black Redstarts from the Asian part of the range was carried out. The revealed differences made it possible to describe a new subspecies from Altai, Tuva, Northern China and Western Mongolia – Phoenicurus ochruros murinus Fedorenko subsp. nov., which is distinguished from the neighboring Turkestan subspecies Ph. o. phoenicuroides by the absence of any contrast in the colour of the head, nape and back; all of which are concolourous dark grey. From Latin, the subspecies name “murinus” is translated as “mouse grey”, which characterises the colour of the upperparts of the bird. A revision of other subspecies of the Asian Black Redstart group was carried out and a map of their distribution was compiled.

Evaluation and retrospective optimization of genomic selection for yield and disease resistance in spring barley

The general applicability of genomic selection (GS) to plant breeding and principles guiding its use have been established by simulation and empirical cross-validation studies. More recently, studies have demonstrated genetic gains over multiple cycles of selection in a variety of crop species. In this study, we provide additional evidence for the effectiveness of GS in an actual breeding program by demonstrating significant gains of 186.1 kg ha−1 and − 1.85 ppm for grain yield and deoxynivalenol, respectively, two unfavorably correlated quantitative traits, across 3 cycles of selection in a spring six-row barley breeding population. With its general effectiveness established, the next step is to increase the accuracy of predictions used in GS and thereby increase genetic gains. For this, we first showed that updating the training population (TP) with phenotyped lines from recent breeding cycles, specifically selected lines, had an overall positive effect on prediction accuracy. Additionally, we investigated four recently proposed algorithms that seek to optimize the composition of a TP. Overall, the optimization algorithms improved prediction accuracy when compared to a randomly selected TP subset of the same size, but which algorithm performed best was dependent on the trait being predicted and other factors discussed within. This retrospective investigation highlights the importance of maintaining and optimizing the TP when using GS in applied breeding to maximize prediction accuracy, thereby maximizing gain from selection and resource utilization efficiency.

Breeding goals and selection effort in the breeding of Lipizzan horses in the stud farm Vucijaka from 1946 to 2015

The Lipizzan horse belongs to the oldest European horse breeds. In the year 1946 the Bosnian Lipizzan state stud farm Vucijak, located next to the town Prnjavor, was founded. The foundation stock originated from the Croatian state stud farms Lipik and Djakovo, and from private owners in Croatia. The breeding goal of Vucijak was to obtain a Lipizzan horse of a smaller body frame suitable for driving and the use as pack horses. The aim of this study was to compare anatomical body measurements of the founder animals with measurements of actual breeding population. From in total 41 horses (10 stallions and 31 mares) following body measurements were taken: height at withers (measured by tape), circumference of chest and circumference of cannon bone forelimb. All horses was 4 years or older at the time of measuring. In order to compare the actual breeding population with the foundation population we extracted comparable data of 17 stallions and 36 mares from the stud book. On the basis of the morphological measures, compactness and bonines index were calculated. The results showed that today's Lipizzan horse of the Vucijak stud are smaller in height at whiters and circumference of chest, while the circumference of cannon bone is larger than documented for founders. The t-test showed a statistically significant difference in the height at whiters and circumference of cannon bone. On the basis of the obtained results, it can be concluded that today's Lipizzan from the Bosnian stud farm Vucijak have a smaller body frame, which confirmed selection success.

Genetic diversity study in Hungarian coldblooded horses

Because of the feeding technology innovation, accelerated transport and communication facilities breeds of high performance breeds replaced local autochone breeds worldwide. These latter species however have an important role in gene conservation. Hungarian cold-blooded horse breeding stock are lacking pedigree, the actual founder breed mares are not known. For this reason, it is an major priority defining the genetic backround of the existing flock, for that breeding could operate with purposeful using of origin maternal founders. In the present study 195 cold-blooded Hungarian mares tail and mane sample were analized. Our analysis was carried out between 15531–15752 base pairs in mithocrondial DNA D-loop region, which reported a total of 222 base pairs. Fourtyone polymorphic sites were determined, which resulted in 39 haplotypes (h=39). The average pairwise differences were k=6.825. High haplotype and nucleotide diversity values were observed (Hd=0.968±0.003, π=0.026±0.003). Based on the previously defined variable positions of haplotypes defined by Jansen et al (2002), we groupped our haplotypes into haplogroups. 23 percent of the studied population (45 mares) belonged to haplogroup F1. Nearly 97% of the analyzed population was classified into one of eight haplogroups defined by Jansen.et al. (2002). This study gives genetic information nearly 25% of the Hungarian population. Another possibility would be patterning more mares or involving more genetic marker in the study which will assuming the possibility of a more comprehensive analysis.

Reproductive timing as a constraint on invasion success in the Ring-necked parakeet (Psittacula krameri)

Climate similarity favors biological invasion, but a match between seasonality in the novel range and the timing of life cycle events of the invader also influences the outcome of species introduction. Yet, phenology effects on invasion success have generally been neglected. Here we study whether a phenological mismatch limits the non-native range of a globally successful invader, the Ring-necked parakeet, in Europe. Given the latitudes at which parakeets have established across Europe, they breed earlier than expected based on breeding dates from the native Asian range. Moreover, comparing the breeding dates of European populations to those of parakeets in the native Asian range, to five native breeding bird species in Europe and to the start of the growing season of four native European trees shows that the discrepancy between expected and actual breeding phenology is greater in northern Europe. In northern European populations, this temporal mismatch appears to have negative effects on hatching success, and on population growth rates in years that are colder than average in the first six months. Phenological mismatch also can explain why parakeets from African populations (that are more likely to breed in autumn) have been poor invaders compared to parakeets from Asia. These lines of evidence support the hypothesis that the reproductive phenology of the Ring-necked parakeet can be a limiting factor for establishment and range expansion in colder climates. Our results provide growing support for the hypothesis that the match between climate seasonality and timing of reproduction (or other important life cycle events) can affect the establishment success, invasive potential and distribution range of introduced non-native species, beyond the mere effect of climate similarity.

Efficiency of genomic selection for breeding population design and phenotype prediction in tomato.

Genomic selection (GS), which uses estimated genetic potential based on genome-wide genotype data for a breeding selection, is now widely accepted as an efficient method to improve genetically complex traits. We assessed the potential of GS for increasing soluble solids content and total fruit weight of tomato. A collection of big-fruited F1 varieties was used to construct the GS models, and the progeny from crosses was used to validate the models. The present study includes two experiments: a prediction of a parental combination that generates superior progeny and the prediction of progeny phenotypes. The GS models successfully predicted a better parent even if the phenotypic value did not vary substantially between candidates. The GS models also predicted phenotypes of progeny, although their efficiency varied depending on the parental cross combinations and the selected traits. Although further analyses are required to apply GS in an actual breeding situation, our results indicated that GS is a promising strategy for future tomato breeding design.

Root plasticity for maintenance of productivity under abiotic stressed soil environments in rice: Progress and prospects

Roots play a number of important roles in crop adaptation to various abiotic stresses such as water stress. However, traits responsible for such adaptation may differ with environments. This paper reviews recent progress in our research on the functional roles of important root traits. We have been paying special attention to drought as well as to soil moisture fluctuations as prevailing water stresses, and the ability of the plant to change its development as environmental conditions change, which is known as phenotypic plasticity. We have been using various rice accessions/mapping populations such as the OryzaSNP panel, chromosome segment substitution lines (CSSL) derived from a Nipponbare and Kasalath cross, and IR64 introgression lines. The results consistently showed that, in addition to deep roots, the plasticity of root system development is a key trait for plant adaptation to water stress. We found that plasticity in the development of the entire root system as a function of the plasticity in lateral root development is important under progressive drought, while plasticity in lateral root development that is associated with aerenchyma formation is important under transient drought-to-waterlogged conditions. We quantitatively showed the contributions of root plasticity to dry matter production and yield through enhanced water uptake under such water stress. We also identified quantitative trait loci (QTLs) that are responsible for root plasticity. The importance of explicitly characterizing the nature of the stresses in the target areas is discussed in relation with designing an ideal root system, which is a primary requirement to define an actual breeding target for improving productivity in abiotic stress-prone soil environments.

Morphological disparity, conservatism, and integration in the canine lower cervical spine: Insights into mammalian neck function and regionalization

The neck skeleton is constituted as a highly mobile, multi-element and multi-joint kinematic chain. This construction leads to a kinematic redundancy on several levels. The problem of coordinating a large number of joints and muscles is solved by reducing the degrees of freedom to only few preferred motor axes. This is achieved by the regionalization of the cervical spine into three functional compartments. However, the neck skeleton traditionally is only partitioned into two units basing on the derived morphology of the two uppermost vertebrae (atlas and axis). To broaden the understanding of the functional morphology and regionalization of the mammalian neck skeleton, the morphology of the lower cervical vertebrae of a variety of different sized breeds of domestic dogs is compared using 3D geometric morphometrics. The shape analysis reveals significant differences among all lower cervical vertebrae. However, the specific shape of each vertebral level is independent of the actual breed and breed size. The individual vertebrae as well as the whole vertebral proportions are highly integrated. Nevertheless, the mid-cervical vertebrae (C3–C5) are more uniform in their shape whereas the lower ones (C6, C7) have a unique morphology. The tripartition of the cervical spine into functional compartments is confirmed for the neck of dogs. The conserved pattern of level specific vertebral shapes suggests that the morphological and functional tripartition of the cervical spine could be a general trait of all mammalians.