Integrated genomic selection for rapid improvement of crops

An increase in the rate of crop improvement is essential for achieving sustained food production and other needs of ever-increasing population. Genomic selection (GS) is a potential breeding tool that has been successfully employed in animal breeding and is being incorporated into plant breeding. GS promises accelerated breeding cycles through a rapid selection of superior genotypes. Numerous empirical and simulation studies on GS and realized impacts on improvement in the crop yields are recently being reported. For a holistic understanding of the technology, we briefly discuss the concept of genetic gain, GS methodology, its current status, advantages of GS over other breeding methods, prediction models, and the factors controlling prediction accuracy in GS. Also, integration of speed breeding and other novel technologies viz. high throughput genotyping and phenotyping technologies for enhancing the efficiency and pace of GS, followed by its prospective applications in varietal development programs is reviewed.     

Oryza coarctata: the name that best reflects the relationships of Porteresia coarctata (Poaceae: Oryzeae)

Oryza coarctata is a herbaceous species that serves as an important source of germplasm for salt tolerance in rice breeding. Despite biosystematic and phylogenetic studies showing that its closest relatives are other species of Oryza, many taxonomists continue to place it in the monospecific genus Porteresia because it is morphologically and ecologically distinct from other species of Ova. Such a treatment obscures the reality of its genetic similarities to Oryza. The authors strongly recommend returning this species to Oryza. This will have the added advantage of ensuring that all those reading about the species will immediately understand its importance to rice breeding.     

Salt-tolerant crops: origins,development, and prospects of the concept

Summary The genetic approach to the problems posed by salt-affected soils and water,i.e., breeding crops resistant to salinity stress, is traced to two principal origins: the European ecological interest in halophytes, and the exigencies of growing crops in the arid and semi-arid lands of the American West. The point is made that breeding for resistance to salinity stress cannot be divorced from breeding for various other desirable traits of mineral plant nutrition and metabolism. A survey is conducted of the existing body of information on breeding for desiderata of mineral nutrition in general and salt tolerance in particular. The prospects of breeding crops for salt tolerance are discussed, with emphasis on a) its relation to breeding for resistance to other mineral stresses; b) field trials; c) collaboration between plant physiologists and geneticist-breeders; and d) extensive exploration of germplasm.     

Interspecific reciprocity explains mobbing behaviour of the breeding chaffinches,Fringilla coelebs

When prey animals discover a predator close by, they mob it while uttering characteristic sounds that attract other prey individuals to the vicinity. Mobbing causes a predator to vacate its immediate foraging area, which gives an opportunity for prey individuals to continue their interrupted daily activity. Besides the increased benefits, mobbing behaviour also has its costs owing to injuries or death. The initiator of mobbing may be at increased risk of predation by attracting the predator's attention, especially if not joined by other neighbouring prey individuals. Communities of breeding birds have always been considered as temporal aggregations. Since an altruist could not prevent cheaters from exploiting its altruism in an anonymous community, this excluded any possibility of explaining mobbing behaviour in terms of reciprocal altruism. However, sedentary birds may have become acquainted since the previous non-breeding season. Migrant birds, forming anonymous communities at the beginning of the breeding season, may also develop closer social ties during the course of the breeding season. We tested whether a male chaffinch, a migrant bird, would initiate active harassment of a predator both at the beginning of the breeding season and a week later when it has become a member of a non-anonymous multi-species aggregation of sedentary birds. We expected that male chaffinches would be less likely to initiate a mob at the beginning of the breeding season when part of an anonymous multi-species aggregation of migratory birds. However, their mobbing activity should increase as the breeding season advances. Our results support these predictions. Cooperation among individuals belonging to different species in driving the predator away may be explained as interspecific reciprocity based on interspecific recognition and temporal stability of the breeding communities.     

The contribution of distant hybridization with decaploid Agropyron elongatum to wheat improvement in China

Wheat is a staple food crop in the world as well as in China. Because of the progress of wheat breeding and other agricultural sci-technologies, the wheat grain yield per unit area has increased more than five folds from 1952 to 2006 in China. The first part of this article briefly reviews the history of wheat breeding in China. Second, the establishment of "Triticum aestivum-Agropyron" distant hybridization system and its contribution to wheat production and breeding in China are summarized. Finally, the future challenges of wheat breeding are discussed, which include how to increase the utilization efficiencies of water, soil nutrient and light energy through breeding.As an example, our research progress on how to increase light use efficiency in wheat through breeding is introduced and discussed.     

Using miniaturized radiotelemetry to discover the breeding grounds of the endangered New Zealand Storm Petrel Fregetta maoriana

Identification of breeding sites remains a critical step in species conservation, particularly in procellariiform seabirds whose threat status is of global concern. We designed and conducted an integrative radiotelemetry approach to uncover the breeding grounds of the critically endangered New Zealand Storm Petrel Fregetta maoriana (NZSP), a species considered extinct before its rediscovery in 2003. Solar‐powered automated radio receivers and hand‐held telemetry were used to detect the presence of birds on three island groups in the Hauraki Gulf near Auckland, New Zealand. At least 11 NZSP captured and radiotagged at sea were detected at night near Te Hauturu‐o‐Toi/Little Barrier Island with the detection of an incubating bird leading to the discovery of the first known breeding site for this species. In total, four NZSP breeding burrows were detected under mature forest canopy and three adult NZSP and two NZSP chicks were ringed. Telemetry data indicated NZSP showed strong moonlight avoidance behaviour over the breeding site, had incubation shifts of approximately 5 days and had a breeding season extending from February to June/July, a different season from other Procellariiformes in the region. Radiotelemetry, in combination with rigorously collected field data on species distribution, offers a valuable technique for locating breeding grounds of procellariiform seabirds and gaining insights into breeding biology while minimizing disturbance to sensitive species or damage to fragile habitat. Our study suggests an avenue for other breeding ground searches in one of the most threatened avian Orders, and highlights the general need for information on the location of breeding sites and understanding the breeding biology in data‐deficient birds.     

Changes in the breeding avifauna of Israel during 2003–2016

Based on information obtained from publications, online material and experienced birdwatchers we describe changes in the breeding avifauna of Israel between 2003 and 2016. We provide details on nine species that were found breeding in Israel during this period for the first time (Common Shelduck, Great Cormorant, Black-winged Kite, Caspian Tern, White-cheeked Tern, Common Wood Pigeon, Black Bush Robin, Basra Reed Warbler, Chiffchaff); two species that were found breeding in Israel after they were not documented breeding for more than 50 years (Great Crested Grebe, Pallid Scops Owl), one species that significantly extended its breeding range in Israel (Striated Heron), and two exotic species that have recently established populations in Israel (Monk Parakeet, Vinous-breasted Starling). This brings the number of bird species breeding in Israel in 2016 to 220. We also report here that out of six new breeding species reported in 2003, three species established breeding populations in Israel, while the other species did not continue to breed in Israel regularly.     

EXTRAPAIR MATE CHOICE AND HONEST SIGNALING IN COOPERATIVELY BREEDING SUPERB FAIRY-WRENS

In many species of monogamous birds females copulate with males other than their social mates, resulting in extrapair fertilizations. Little is known about how females choose extrapair mates and whether the traits used to choose them are reliable indicators of male quality. Here we identify a novel male trait associated with extra-group mating success in the superb fairy-wren (Malurus cyaneus), a cooperatively breeding bird with one of the highest known frequencies of extra-group mating. Female fairy-wrens chose extra-group mates that molted earlier into breeding plumage. Males molted up to five months before the breeding season began, and only males that molted at least one month prior to its onset gained any extra-group fertilizations. This conclusion held after controlling statistically for the effect of age and social status on molt date. Once males acquired breeding plumage, they began courtship display to females on other territories. Thus, some males were displaying to females for several months before the breeding season began. This extraordinarily long period of advertisement by males may be facilitated by the long-term ownership of territories. We suggest that early acquisition of breeding plumage or the subsequent display behavior can be reliable cues for mate choice because they are costly to acquire or maintain.     

Cooperative Breeding and Group Structure in the Lake Tanganyika Cichlid Neolamprologus savoryi

As yet, cooperative breeding has been described only for some fish species. However, evidence is accumulating that it is widespread among Lake Tanganyika cichlids. We studied the cooperative breeding system of the substrate breeding cichlid Neolamprologus savoryi. Breeding groups typically consisted of a large breeding male with one to four breeding females and three to 33 helpers (mean group size: 14.3 members). Group size was significantly related to breeding male and female body sizes, and larger males had more breeding females and larger sized male helpers. The size of the largest female in the group was positively related to the number and sizes of secondary breeding females and female helpers. In case of multiple breeding females, these females usually divided the group's territory into sub‐territories, each with its own helpers (subgroups). Interspersed between groups, independent fish were detected defending an individual shelter (4.4% of all fish). In 9% of the groups no breeding female was present. All group members participated in territory defence and maintenance, and showed submissive behaviours to larger group members. As expected, the level of between‐subgroup conflicts was high compared with the level of within‐subgroup conflicts. We compare these results with data available from other cooperatively breeding fishes.     

低功率CO2激光、TDP及其它红外辐射对鱼类(亲鱼)生长发育影响的研究(Ⅱ)

应用低功率CO2激光和TDP红外辐射辐照鲤、鲫、草鱼、鲢、鳙等的孵化期鱼卵、稚鱼、鱼苗和鱼种以选育繁殖用亲鱼,并在繁殖期对产卵池内的雌雄亲鱼进行辐照处理,以观察经选育的亲鱼的繁殖力和子代苗种的相关遗传性能。经与空白对照组和促长剂对照组的亲鱼相关的性能进行对比,经辐射处理的亲鱼生长发育正常,品种特征显现明显优势,繁殖力和抗病抗逆力增强,繁殖用期限延长。对鱼类的低功率激光和TDP辐照系列技术进行了长达10年以上的远期效果进行了追踪观察,未发现亲鱼和子代鱼苗、鱼种的致畸、致癌变和诸多遗传退化现象。     

Cassava breeding: opportunities and challenges

Although cassava is a major food crop, its scientific breeding began only recently compared with other crops. Significant progress has been achieved, particularly in Asia where cassava is used mainly for industrial processes and no major biotic constraints affect its productivity. Cassava breeding faces several limitations that need to be addressed. The heterozygous nature of the crop and parental lines used to generate new segregating progenies makes it difficult to identify parents with good breeding values. Breeding so far has been mainly based on a mass phenotypic recurrent selection. There is very little knowledge on the inheritance of traits of agronomic relevance. Several approaches have been taken to overcome the constraints in the current methodologies for the genetic improvement of cassava. Evaluations at early stages of selection allow for estimates of general combining ability effect or breeding values of parental lines. Inbreeding by sequential self-pollination facilitates the identification of useful recessive traits, either already present in the Manihot gene pool or induced by mutagenesis.     

Reproduction of the least weasel in captivity: basic observations and the influence of food availability

The least weaselMustela nivalis nivalis Linnaeus, 1766 is unique among carnivores because of its small body size and capacity for fast reproduction. It has been suggested to be the main agent for maintaining cyclic fluctuations in northern vole populations, largely based on its high reproductive potential and dependence on small rodents. This study describes basic reproductive data on the least weasel obtained during a captive breeding program. In the experiments, food availability was manipulated at the onset of breeding. Altogether, 65 litters were born during the 5-year study. The mean litter size was 5.1 (in 53 litters of known litter size), the most common litter size being six. The sex ratio of weaned young was not biased from 1∶1. The median date of birth was June 4. Food manipulations did not affect mating frequency suggesting that the observation of failure in breeding in years of low abundance of small mammals is due to mortality of embryos or young before weaning, but not due to avoidance of breeding at low food availability. In this respect, weasels differ from other main vole predators, owls and raptors, which often skip breeding if small mammals are scarce.     

Young But Not Old Adult African Striped Mice Reduce Their Activity in the Dry Season When Food Availability is Low

An individual′s survival and fitness depend on its ability to effectively allocate its time between competing behaviors. Sex, social tactic, season and food availability are important factors influencing activity budgets. However, few field studies have tested their influences. The African striped mouse (Rhabdomys pumilio) lives in highly seasonal habitats in southern Africa, and individuals can adopt different social tactics. We investigated seasonal changes in activity budgets of different tactics and predicted that individuals will reduce their activity in the non‐breeding season to save energy when food availability is low and that young non‐breeding adults (‘philopatrics’) invest mainly in activities related to gaining body mass to increase survival probability. We predicted old adults (‘breeders’), which bred during the previous breeding season, to invest mainly in maintenance of their social status. We conducted 90 focal observations during the non‐breeding season and 73 during the breeding season. Activity budgets of striped mice were season and tactic specific, with philopatrics, but not breeders, reducing activity when food availability was low, possibly to decrease energy expenditure. Philopatrics of both sexes foraged and basked more in the breeding season than during the non‐breeding season. Male philopatrics gained body mass and female philopatrics maintained their body mass in both seasons. Sex‐specific differences occurred during the breeding season, when female breeders foraged more than male breeders, while male breeders chased other individuals more than female breeders. These findings indicate that individuals adopting different social tactics display distinct behaviors to fulfill tactic‐specific energetic needs .     

Accounting for competition in genetic analysis, with particular emphasis on forest genetic trials

Available experimental evidence suggests that there are genetic differences in the abilities of trees to compete for resources, in addition to non-genetic differences due to micro-site variation. The use of indirect genetic effects within the framework of linear mixed model methodology has been proposed for estimating genetic parameters and responses to selection in the presence of genetic competition. In this context, an individual’s total breeding value reflects the effects of its direct breeding value on its own phenotype and its competitive breeding value on the phenotype of its neighbours. The present study used simulated data to investigate the relevance of accounting for competitive effects at the genetic and non-genetic levels in terms of the estimation of (co)variance components and selection response. Different experimental designs that resulted in different genetic relatedness levels within a neighbourhood and survival were other key issues examined. Variances estimated for additive genetic and residual effects tended to be biased under models that ignored genetic competition. Models that fitted competition at the genetic level only also resulted in biased (co)variance estimates for direct additive, competitive additive and residual effects. The ability to detect the correct model was reduced when relatedness within a neighbourhood was very low and survival decreased. Selection responses changed considerably between selecting on breeding value estimates from a model ignoring genetic competition and total breeding estimates using the correct model. Our results suggest that considering a genetic basis to competitive ability will be important to optimise selection programmes for genetic improvement of tree species.     

Marker-based estimation of the coefficient of coancestry in hybrid breeding programmes

Molecular markers allow to estimate the pairwise relatedness between the members of a breeding pool when their selection history is no longer available or has become too complex for a classical pedigree analysis. The field of population genetics has several estimation procedures at its disposal, but when the genotyped individuals are highly selected inbred lines, their application is not warranted as the theoretical assumptions on which these estimators were built, usually linkage equilibrium between marker loci or even Hardy–Weinberg equilibrium, are not met. An alternative approach requires the availability of a genotyped reference set of inbred lines, which allows to correct the observed marker similarities for their inherent upward bias when used as a coancestry measure. However, this approach does not guarantee that the resulting coancestry matrix is at least positive semi-definite (psd), a necessary condition for its use as a covariance matrix. In this paper we present the weighted alikeness in state (WAIS) estimator. This marker-based coancestry estimator is compared to several other commonly applied relatedness estimators under realistic hybrid breeding conditions in a number of simulations. We also fit a linear mixed model to phenotypical data from a commercial maize breeding programme and compare the likelihood of the different variance structures. WAIS is shown to be psd which makes it suitable for modelling the covariance between genetic components in linear mixed models involved in breeding value estimation or association studies. Results indicate that it generally produces a low root mean squared error under different breeding circumstances and provides a fit to the data that is comparable to that of several other marker-based alternatives. Recommendations for each of the examined coancestry measures are provided.     

Relationship between breeding and wintering ranges in Palaearctic-African migrants

During the northern winter, Palaearctic migrant species are not evenly distributed within sub-Saharan Africa. Species numbers are greatest in a belt of savannah, lying south of the Sahara, and decline southwards. For any one latitude, species numbers are also greater in the east of Africa than in the west. Only about 3% of 187 species winter exclusively south of the equator, but other species migrate from north to south during the course of the northern winter.
For 62 Palaearctic species which winter entirely in Africa, the areas of breeding and wintering ranges are strongly correlated. With some exceptions, species with the largest breeding ranges also have the largest wintering ranges. However, in 69% of species, the breeding range is larger than the wintering range, whereas in 31% of species the wintering range is larger. On average, the wintering ranges of 57 landbird species cover about two-thirds the area of their breeding ranges, and in many species only parts of the wintering range may be occupied at any one time. This implies that the per area carrying capacity of African wintering areas is greater than that of Eurasian breeding areas.
The general correlation between the sizes of breeding and wintering ranges may have its basis in ecology, with generalists able to occupy wider areas than specialists in both breeding and winter quarters. At the same time, the correlation may result partly from an effect of numbers on range size, in that species which have a wide range at one time of the year may then achieve large numbers which occupy a wide range at the other time of year.     

Concentrations of insulin-like growth factor-I in adult male white-tailed deer (Odocoileus virginianus): associations with serum testosterone, morphometrics and age during and after the breeding season

Our understanding of insulin-like growth factor-I (IGF-I) in cervids has been limited mostly to its effects on antler development in red deer (Cervus elaphus), roe deer (Capreolus capreolus), fallow deer (Dama dama), and pudu (Pudu puda). Although IGF-I has been found to play a critical role in reproductive function of other mammals, its role in reproduction of deer is unknown. The objectives of the present study were to determine if serum levels of IGF-I change during the breeding season, assess whether age influences serum IGF-I, compare levels of IGF-I measured during and following the breeding season, and determine if IGF-I is associated with body and antler characteristics in free-ranging adult, male white-tailed deer (Odocoileus virginianus). We collected serum and morphometric data from hunter-harvested and captured white-tailed deer to investigate these objectives. Mean level of serum IGF-I during the breeding season was 63.6 ng/ml and was greatest in deer between 2.5 and 5.5 years old (57.4-79.9 ng/ml). Levels of serum IGF-I decreased by approximately 40% as the breeding season progressed, but levels were less in deer following the breeding season (34.6 ng/ml). Both body and antler size were associated positively with IGF-I when controlling for age. Serum testosterone was also associated positively with IGF-I. Levels of serum testosterone during the breeding season generally increased with age from 4.82 (1.5 years old) to 18.79 ng/dl (5.5 years old), but decreased thereafter. These data suggest that IGF-I may be an important hormone in breeding, male white-tailed deer.     

能源木薯高淀粉抗逆分子育种研究进展与展望

木薯(Manihot esculenta Crantz)是全球重要的粮食作物,也是我国非粮生物质能源发展的主要原材料。长期以来,传统杂交育种是木薯新品种培育的主要手段。随着全球生态的变化和木薯产业发展的推进,需要加速培育抗逆能力强、高淀粉的木薯新品种,因此,利用基因工程针对特定性状开展品种创新表现出巨大的潜力。随着组学技术的发展,在木薯基础研究领域,特别是针对储藏根发育、淀粉富集、逆境响应与调控等方面的研究逐步深入。强化木薯基础理论研究和发展应用技术,对推动能源木薯的产业化发展具有重要意义。     

Identifying potential breeding sites for the stone curlew (Burhinus oedicnemus) in the UK

The stone curlew (Burhinus oedicnemus) is one of the rarest breeding birds in the UK with an estimated breeding population of under 300 pairs. In the UK a marked decrease in the numbers has occurred, mainly due to habitat change or loss, resulting in the bird no longer breeding on many of its traditional nesting grounds. Using a Geographic Information System we define potential breeding areas in a landscape known to historically support a stone curlew breeding population. With an understanding of the birds’ abiotic nesting requirements, we model optimal locations for potential breeding sites for the bird, using known historical breeding data to verify the selection process. In total, we identify 424 parcels of land (2866 hectares) providing the critical habitat requirements for the stone curlew in the overall study area, 323 (1958 hectares) of which correspond with the known historic breeding distribution of the bird. We conclude that the modelling approach outlined is valuable in the identification of potential breeding sites for the stone curlew and that the model could be operated in tandem with agri-environment payments such as those offered within the Countryside Stewardship Scheme, in an attempt to focus these payments upon areas which will deliver maximum nature conservation potential. In addition we suggest that, subject to appropriate data availability, the approach outlined be applied to other species of high-conservation concern, particularly those which are currently under consideration for introduction or re-introduction programmes.