Identification of new cotton fiber-quality QTL by multiple genomic analyses and development of markers for genomic breeding

Cotton fiber is one of the main raw materials for the textile industry.In recent years,many cotton fiber quality QTL have been identified,but few were applied in breeding.In this study,a genome wide association study(GWAS)of fiber-quality traits in 265 upland cotton breeding intermediate lines(GhBreeding),combined with genome-wide selective sweep analysis(GSSA)and genomic selection(GS),revealed 25 QTL.Most of these QTL were ignored by only using GWAS.The CRISPR/Cas9 mutants of GhMYB_D13 had shorter fiber,which indicates the credibility of QTL to a certain extent.Then these QTL were verified in other cotton natural populations,5 stable QTL were found having broad potential for application in breeding.Additionally,among these 5 stable QTL,superior genotypes of 4 showed an enrichment in most improved new varieties widely cultivated currently.These findings provide insights for how to identify more QTL through combined multiple genomic analysis to apply in breeding.

Selection and application of four QTLs for grain protein content in modern wheat cultivars

The grain protein content(GPC)is the key parameter for wheat grain nutritional quality.This study conducted a resampling GWAS analysis using 406 wheat accessions across eight environments,and identified four previously reported GPC QTLs.An analysis of 87 landraces and 259 modern cultivars revealed the loss of superior GPC haplotypes,especially in Chinese cultivars.These haplotypes were preferentially adopted in different agroecological zones and had broad effects on wheat yield and agronomic traits.Most GPC QTLs did not significantly reduce yield,suggesting that high GPC can be achieved without a yield penalty.The results of this study provide a reference for future GPC breeding in wheat using the four identified QTLs.

Breeding of Anti-diarrhea Gene in Local and Exotic Pig Breeds in Guizhou Province

[Objectives]This study was conducted to breed special pig breeds resistant to diarrhea by using modern biotechnology.[Methods]From Guizhou local breeds,such as Nuogu pigs,Kele pig,Yorkshire pigs and Duroc pigs,190 samples were collected for the analysis of anti-diarrhea gene.[Results]The anti-diarrhea genotype frequency of Kele pigs was 70.00%,which was higher than that of Nuogu pigs(67.37%)and Yorkshire pigs(Yorkshire pigs and Duroc pigs)(50.59%).The favorable anti-diarrhea gene of all Nuogu pigs,Kele pigs,and Yorkshire pigs and Duroc pigs was G,with gene frequencies of 0.7355,0.8368 and 0.8500,respectively,and the frequencies of allele A were 0.2645,0.1632 and 0.1500,respectively.In the process of generation selection,combination selection of GG♂×GG♀,GG♂×GA♀,GA♂×GG♀and GA♂×GA♀was conducted,and GG individuals were selected while gradually phasing out GA and AA individuals.The anti-diarrhea genotypes of 98 pigs in the offspring were tested,and it was found that the frequency of genotype GG was greatly improved,and the frequencies in Nuogu pigs,Kele pigs,Yorkshire pigs and Duroc pigs were increased to 73.91%,81.82%,85.25%and 66.67%respectively,thus forming a special anti-diarrhea breed.[Conclusions]This study provides a basis for selecting excellent breeding pigs,establishing core populations and screening resistance genes in the core populations and their offspring.

Selective footprints and genes relevant to cold adaptation and other phenotypic traits are unscrambled in the genomes of divergently selected chicken breeds

Background The genomes of worldwide poultry breeds divergently selected for performance and other phenotypic traits may also be affected by,and formed due to,past and current admixture events.Adaptation to diverse environments,including acclimation to harsh climatic conditions,has also left selection footprints in breed genomes.Results Using the Chicken 50K_CobbCons SNP chip,we genotyped four divergently selected breeds:two aboriginal,cold tolerant Ushanka and Orloff Mille Fleur,one egg-type Russian White subjected to artificial selection for cold tolerance,and one meat-type White Cornish.Signals of selective sweeps were determined in the studied breeds using three methods:(1)assessment of runs of homozygosity islands,(2)F_(ST) based population differential analysis,and(3)haplotype differentiation analysis.Genomic regions of true selection signatures were identified by two or more methods or in two or more breeds.In these regions,we detected 540 prioritized candidate genes supplemented them with those that occurred in one breed using one statistic and were suggested in other studies.Amongst them,SOX5,ME3,ZNF536,WWP1,RIPK2,OSGIN2,DECR1,TPO,PPARGC1A,BDNF,MSTN,and beta-keratin genes can be especially mentioned as candidates for cold adaptation.Epigenetic factors may be involved in regulating some of these important genes(e.g.,TPO and BDNF).Conclusion Based on a genome-wide scan,our findings can help dissect the genetic architecture underlying various phenotypic traits in chicken breeds.These include genes representing the sine qua non for adaptation to harsh environments.Cold tolerance in acclimated chicken breeds may be developed following one of few specific gene expression mechanisms or more than one overlapping response known in cold-exposed individuals,and this warrants further investigation.

Marker-assisted selection to pyramid Fusarium head blight resistance loci Fhb1 and Fhb2 in the high-quality soft wheat cultivar Yangmai 15

Fusarium head blight(FHB)is one of the most detrimental wheat diseases which greatly decreases the yield and grain quality,especially in the middle and lower reaches of the Yangtze River of China.Fhb1 and Fhb2 are two major resistance loci against Fusarium graminearum.Yangmai 15(YM15)is one of the most popular varieties in the middle and lower reaches of the Yangtze River,and it has good weak gluten characters but poor resistance to FHB.Here we used Fhb1 and Fhb2 to improve the FHB resistance of YM15 by a molecular marker-assisted selection(MAS)backcrossing strategy.The selection of agronomic traits was performed for each generation.We successfully selected seven introgressed lines which carry homozygous Fhb1 and Fhb2 with significantly higher FHB resistance than the recurrent parent YM15.Three of the introgressed lines had agronomic and quality characters that were similar to YM15.This study demonstrates that the pyramiding of Fhb1 and Fhb2 could significantly improve the FHB resistance in wheat using the MAS approach.

Study on Breeding Practices and Reproductive Performance of Black-Head Somali Sheep under Traditional Management System: The Case of Awbarre District, Eastern Ethiopia

The study was conducted in the Awbarre district of the Fafen zone of the Somali regional state of Ethiopia. The objective of the study was to assess the breeding practices and reproductive performance of Black-head Somali sheep under a traditional management system. Purposive and simple random sampling techniques were used to select targeted kebeles and households, respectively. A total of 120 households were selected from four kebeles, each of 30 households, based on the production system and sheep population. Semi-structured questionnaires, group discussions, key informants interviews and field observations were used to generate the required data. The primary purpose of keeping sheep was for income generation, followed by saving as a future asset. The majority (89.2%) of the respondents separated male and female animals during herding. The selection criteria for breeding rams were appearance, growth, pedigree, and color while for breeding ewes were appearance, adaptability, pedigree, color, and lamb growth. The overall weaning age of Black-head Somali sheep in the study area was 3.7 months for both males & females. The castration of male sheep was common for the purpose of fattening, fattening with breeding control and breeding control as well. The castration is mainly performed during the summer and autumn and the methods of castration were both traditional and modern methods, the traditional castration method being the most important one in pastoral areas. The age of sexual maturity was 7.64 months for rams and 8.97 months for ewe’s male and female lambs in the pastoral area and 8.42 & 8.38 for rams & ewes in agro-pastoral and overall lambing interval was 11 months. On average, the ewe of Black-head Somali sheep in pastoral & agro-pastoral could produce 9.49 & 9.57 lambs, respectively in their lifetime. As the pastoralists and agro-pastoralists indicated the source of the breeding ram was their own, so the exchange of breeding ram is recommended to minimize the risk of inbreeding and further studies of on-farm performance investigation would be necessary to be carried out so as to understand the uniqueness of the breed better.

Examining the Burden Reduction Policy for Primary and Secondary School Teachers in China:A Framework Analysis Centered on the Rational Selection of Institutional Doctrine

The“burden reduction”policy aims to reduce the workload of primary and secondary school teachers to alleviate their burdens.While it has improved the quality of teachers,implementation challenges still exist.This study utilizes rational choice institutionalism and Ostrom’s institutional analysis and development framework to examine the policy.By considering the preferences of the Ministry of Education,local governments,schools,and teachers,it explores interactions and outcomes,identifies challenges,and provides policy suggestions.

Improving the phenotypic expression of rice genotypes:Rethinking “intensification” for production systems and selection practices for rice breeding

Intensification in rice crop production is generally understood as requiring increased use of material inputs: water, inorganic fertilizers, and agrochemicals. However, this is not the only kind of intensification available. More productive crop phenotypes, with traits such as more resistance to biotic and abiotic stresses and shorter crop cycles, are possible through modifications in the management of rice plants, soil, water, and nutrients, reducing rather than increasing material inputs. Greater factor productivity can be achieved through the application of new knowledge and more skill, and(initially) more labor, as seen from the System of Rice Intensification(SRI), whose practices are used in various combinations by as many as 10 million farmers on about 4 million hectares in over 50 countries. The highest yields achieved with these management methods have come from hybrids and improved rice varieties, confirming the importance of making genetic improvements. However,unimproved varieties are also responsive to these changes, which induce better growth and functioning of rice root systems and more abundance, diversity, and activity of beneficial soil organisms. Some of these organisms as symbiotic endophytes can affect and enhance the expression of rice plants' genetic potential as well as their phenotypic resilience to multiple stresses, including those of climate change. SRI experience and data suggest that decades of plant breeding have been selecting for the best crop genetic endowments under suboptimal growing conditions, with crowding of plants that impedes their photosynthesis and growth, flooding of rice paddies that causes roots to degenerate and forgoes benefits derived from aerobic soil organisms, and overuse of agrochemicals that adversely affect these organisms as well as soil and human health. This review paper reports evidence from research in India and Indonesia that changes in crop and water management can improve the expression of rice plants' genetic potential, thereby creating more productive and robustphenotypes from given rice genotypes. Data indicate that increased plant density does not necessarily enhance crop yield potential, as classical breeding methods suggest. Developing cultivars that can achieve their higher productivity under a wide range of plant densities—breeding for density-neutral cultivars using alternative selection strategies—will enable more effective exploitation of available crop growth resources. Density-neutral cultivars that achieve high productivity under ample environmental growth resources can also achieve optimal productivity under limited resources, where lower densities can avert crop failure due to overcrowding. This will become more important to the extent that climatic and other factors become more adverse to crop production. Focusing more on which management practices can evoke the most productive and robust phenotypes from given genotypes is important for rice breeding and improvement programs since it is phenotypes that feed our human populations.

Nest-site selection and breeding ecology of Streaked Wren-Babbler(Napothera brevicaudata)in a tropical limestone forest of southern China

Background: The breeding information of most birds in Asian tropical areas,especially in limestone forests,is still poorly known.The Streaked Wren-Babbler(Napothera brevicaudata) is an uncommon tropical limestone bird with a small range.We studied its nest-site selection and breeding ecology,in order to understand the adaptations of birds to the conditions of tropical limestone forest in southern China.Methods: We used methods of systematical searching and parent-following to locate the nests of the Streaked Wren-Babbler.We measured characteristics of nest sites and rock cavities.Data loggers and video cameras were used to monitor the breeding behavior.Results: All the observed nests of the Streaked Wren-Babbler were placed in natural shallow cavities or deep holes in large boulders or limestone cliffs.The great majority(96.6%) of Streaked Wren-Babbler nests had three eggs with an average fresh weight of 3.46-± 0.43 g(n = 36,range 2.52-4.20 g).Most(80.4%) females laid their first eggs between March and April(n = 46).The average incubation and nestling period of the Streaked Wren-Babbler was 10.2 range 9-11 days),respectively.Most(87.9%) nests h± 0.4 days(n = 5,range 1011 days) and 10.5 ± 0.8 days(n = 6,ad at least one nestling fledge between 2011 and 2013(n = 33).Conclusions: Our study suggests that several features of the breeding ecology of the Streaked Wren-Babbler,including building nests in rocky cavities,commencing breeding earlier than most species,and reducing foraging times during the incubation period,are well-adapted to the unique habitat of tropical limestone forest.

Rice Heat Tolerance Breeding: A Comprehensive Review and Forward Gaze

The yield potential of rice is seriously affected by heat stress due to climate change. Since rice is a staple food globally, it is imperative to develop heat-resistant rice varieties. Thus, a thorough understanding of the complex molecular mechanisms underlying heat tolerance and the impact of high temperatures on various critical stages of the crop is needed. Adoption of both conventional and innovative breeding strategies offers a long-term advantage over other methods, such as agronomic practices, to counter heat stress. In this review, we summarize the effects of heat stress, regulatory pathways for heat tolerance, phenotyping strategies, and various breeding methods available for developing heat-tolerant rice. We offer perspectives and knowledge to guide future research endeavors aimed at enhancing the ability of rice to withstand heat stress and ultimately benefit humanity.

THE STUDY OF EARLY DEVELOPMENT AND EVOLUTION OF Torrentophryne aspinia

Torrentophryne aspinia is a new kind of toads discovered in China recently, it lives in the forest floor in West Yunnan, the most important things for this kind of species is that they have a kind of torrent-adapted tadpoles which have abdominal suckers and can adhere to the surfaces of rocks in moving waters. In this article, we described the forming procedures of abdominal sucker and some breeding behaviors, habitats and habits. After comparing with those of other toads, it is confirmed that Torrentophryne should be a new valid genus, it is derived from ancestor toads because of adaptation to the torrent habitats, by the forming of torrent -adapted organ-abdominal sucker in the early development.

Strategies and Suggestions for the Development of Mechanized Rapeseed Production in Sichuan

Mechanization is the future direction of rapeseed production in Sichuan. A series of technology tests for rapeseed mechanized production have been carried out in terms of variety selection, key agronomic measures and machinery in the main production area of Sichuan in recent years. In the research, the agronomic techniques, including variety selection for mechanical production, key agronomic measures and mechanical harvesting were analyzed. Based on the present condi- tions, strategy and suggestions for the development of mechanized rapeseed produc- tion in Sichuan also were presented.

Selection of wide compatible restorer lines and their application in hybrid rice breeding

Since the middle of 1980’s, wide compatibility(WC) rice lines have been screened by ricebreeders in China and applied in hybrid ricebreeding program. Several WC lines such asPecos, T984, Lunhui 422, and 02428 withideal agronomic characters were identified. Weincorporated the WC gene into restorer linesby crossing these japonica WC lines with ob-tained indica lines. Some WC restorer lineswith indica-japonica medium type were ob-tained and their application value in intersub-specific hybrid rice breeding were evaluated. 1. Effect of crossing methods on selectionefficiencies of WC restorer lines

Current Situation and Development Countermeasures of Alpaca Breeding

This paper briefly introduces the biological characteristics and value of alpaca breeding,reviews the development of alpaca breeding,describes the global distribution of alpaca and the current situation of alpaca breeding in the introduction of well-bred,indicates the technology of feeding,managing and deep processing.And finally some countermeasures for future development of alpaca breeding in China are put forward.

Flexible nest site selection of the endangered Oriental Storks(Ciconia boyciana):Trade-off from adaptive strategies

Nest site selection is a vital component of bird reproduction success,and an adaptive behavior conducted to decrease nest predation risk with avoiding external disturbances.Understanding patterns of nest site selection can provide insights into how species adapt to changes in their habitat and has important conservation implications.In this study,we used microhabitat variables and multi-scale data with a field survey of nest occurrence to determine nest site selection patterns and adaptive strategies of the breeding Oriental Storks(Ciconia boyciana)in different nest areas.Results demonstrate that the nest site microhabitat characteristics of the breeding Oriental Storks significantly differed among the three nesting areas,and nest height was higher in the middle and lower Yangtze River floodplain than in the Northeast China and Bohai Bay nest areas.The food resources and intensity of human disturbance had the greatest effects on the nest site selection of the breeding Oriental Storks.The intensity of human disturbance was positively correlated with the nest height of the breeding Oriental Storks in Bohai Bay and the middle and lower Yangtze River floodplain;however,nest height decreased with the abundance of food resources in the Northeast China nest area.Our findings indicate that the nest site selection patterns of Oriental Storks showed flexible adaptive strategies.In safer environments,nests were lower and closer to food resources,which allows parent storks to invest more in the nestlings.However,in areas where human activity was intense,nests were higher to ensure the safety of their offspring.Some measures that could be taken to improve the breeding habitat of Oriental Storks include increasing the percentage of wetland areas in nesting areas to enhance food resources availability and setting artificial nests at suitable heights in potential nesting grounds to encourage nesting.Finally,the establishment of soft barriers around the nesting areas could increase the safety of nests.

3D genome organization and its study in livestock breeding

Eukaryotic genomes are hierarchically packaged into cell nucleus,affecting gene regulation.The genome is organized into multiscale structural units,including chromosome territories,compartments,topologically associating domains(TADs),and DNA loops.The identification of these hierarchical structures has benefited from the development of experimental approaches,such as 3C-based methods(Hi-C,ChIA-PET,etc.),imaging tools(2D-FISH,3D-FISH,Cryo-FISH,etc.)and ligation-free methods(GAM,SPRITE,etc.).In recent two decades,numerous studies have shown that the 3D organization of genome plays essential roles in multiple cellular processes via various mechanisms,such as regulating enhancer activity and promoter-enhancer interactions.However,there are relatively few studies about the 3D genome in livestock species.Therefore,studies for exploring the function of 3D genomes in livestock are urgently needed to provide a more comprehensive understanding of potential relationships between the genome and production traits.In this review,we summarize the recent advances of 3D genomics and its biological functions in human and mouse studies,drawing inspiration to explore the 3D genomics of livestock species.We then mainly focus on the biological functions of 3D genome organization in muscle development and its implications in animal breeding.

Use of genomic selection and breeding simulation in cross prediction for improvement of yield and quality in wheat (Triticum aestivum L.)

In wheat breeding, it is a difficult task to select the most suitable parents for making crosses aimed at the improvement of both grain yield and grain quality. By quantitative genetics theory,the best cross should have high progeny mean and large genetic variance, and ideally yield and quality should be less negatively or positively correlated. Usefulness is built on population mean and genetic variance, which can be used to select the best crosses or populations to achieve the breeding objective. In this study, we first compared five models(RR-BLUP, Bayes A, Bayes B, Bayes ridge regression, and Bayes LASSO) for genomic selection(GS) with respect to prediction of usefulness of a biparental cross and two criteria for parental selection, using simulation. The two parental selection criteria were usefulness and midparent genomic estimated breeding value(GEBV). Marginal differences were observed among GS models. Parental selection with usefulness resulted in higher genetic gain than midparent GEBV. In a population of 57 wheat fixed lines genotyped with 7588 selected markers, usefulness of each biparental cross was calculated to evaluate the cross performance, a key target of breeding programs aimed at developing pure lines. It was observed that progeny mean was a major determinant of usefulness, but the usefulness ratings of quality traits were more influenced by their genetic variances in the progeny population. Near-zero or positive correlations between yield and major quality traits were found in some crosses, although they were negatively correlated in the population of parents. A selection index incorporating yield, extensibility, and maximum resistance was formed as a new trait and its usefulness for selecting the crosses with the best potential to improve yield and quality simultaneously was calculated. It was shown that applying the selection index improved both yield and quality while retaining more genetic variance in the selected progenies than the individual trait selection. It was concluded that combining genomic selection with simulation allows the prediction of cross performance in simulated progenies and thereby identifies candidate parents before crosses are made in the field for pure-line breeding programs.

The essential roles of sugar metabolism for pollen development and male fertility in plants

Sugar metabolism plays an essential role in plant male reproduction. Defects in sugar metabolism during anther and pollen development often result in genic male sterility(GMS). In this review, we summarize the recent progresses of the sugar metabolism-related GMS genes and their roles during plant anther and pollen development, including callose wall and primexine formation, intine development, pollen maturation and starch accumulation, anther dehiscence, and pollen germination and tube growth. We predict 112 putative sugar metabolic GMS genes in maize based on bioinformatics and RNA-seq analyses, and most of them have peak expression patterns during middle or late anther developmental stages.Finally, we outline the potential applications of sugar metabolic GMS genes in crop hybrid breeding and seed production. This review will deepen our understanding on sugar metabolic pathways in controlling pollen development and male fertility in plants.

Effects of Tebufenozide on the Biological Characteristics of Beet Armyworm (Spodoptera exigua Hübner) and Its Resistance Selection

In this article, the selection of tebufenozide to beet armyworm （Spodoptera exigua Htibner） was studied by the treatments to alternative generations＇ 3rd-instar larvae with LC50 dose and to continuous generations＇ larvae with LC10 dose; the effects of tebufenozide on the biological characteristics of current and subsequent generations were examined by the treatments to 3rd-instar larvae and egg pods in different concentrations. After treatments with LC50 dose till F11, the toxicity of tebufenozide to beet armyworm had no significant change, whereas the pupation rate, pupal weight, and fecundity were reduced markedly. After treatments with LC10 dose till Fl9, the beet armyworm only developed 3.52-fold resistance, and the main biological characteristics were nearly accordant in each generation. The livability was reduced 72 h later after treatments to 3rd-instar larvae, respectively in 2.5-40 μg mL^-1, and larval duration, pupation rate, and pupal weight changed considerably with the increase in concentrations. The fecundity, larval livability, larval weight and pupal weight of subsequent generations were reduced as the dose increased over 10 μg mL^-1. The hatching rate of egg pods did not differ with that of the controls obviously after treatment in 10-300 μg mL^-1. But the larval livability, larval weight and pupal weight were reduced when eggs were exposed to 50 μg mL^-1 dose or more. The results indicated that tebufenozide had low resistance risk to the current and subsequent generations of beet armyworm even if tebufenozide had significant effects on the biological characteristics of this insect.