Evaluating the performance of genomic selection on purebred population by incorporating crossbred data in pigs

Genomic selection(GS)has been widely used in livestock,which greatly accelerated the genetic progress of complex traits.The population size was one of the significant factors affecting the prediction accuracy,while it was limited by the purebred population.Compared to directly combining two uncorrelated purebred populations to extend the reference population size,it might be more meaningful to incorporate the correlated crossbreds into reference population for genomic prediction.In this study,we simulated purebred offspring(PAS and PBS)and crossbred offspring(CAB)base on real genotype data of two base purebred populations(PA and PB),to evaluate the performance of genomic selection on purebred while incorporating crossbred information.The results showed that selecting key crossbred individuals via maximizing the expected genetic relationship(REL)was better than the other methods(individuals closet or farthest to the purebred population,CP/FP)in term of the prediction accuracy.Furthermore,the prediction accuracy of reference populations combining PA and CAB was significantly better only based on PA,which was similar to combine PA and PAS.Moreover,the rank correlation between the multiple of the increased relationship(MIR)and reliability improvement was 0.60-0.70.But for individuals with low correlation(Cor(Pi,PA or B),the reliability improvement was significantly lower than other individuals.Our findings suggested that incorporating crossbred into purebred population could improve the performance of genetic prediction compared with using the purebred population only.The genetic relationship between purebred and crossbred population is a key factor determining the increased reliability while incorporating crossbred population in the genomic prediction on pure bred individuals.

Theoretical investigations of population trapping phenomena in atomic four-color,three-step photoionization scheme

The four-color three-step selective photoionization process of atom is very important in laser isotope separation technology.The population trapping phenomena and their influences are studied theoretically in monochromatic and non-monochromatic laser fields based on the density matrix theory in this work.Time evolutions of the photoionization properties of the four-color,three-step process are given.The population trapping effects occur intensely in monochromatic excitation,while it gradually turns weak as the laser bandwidth increases.The effects of bandwidth,Rabi frequency,time delay,and frequency detuning on the population trapping effect are investigated in monochromatic and non-monochromatic laser fields.The effects of laser process parameters and atomic parameters on the effective selective photoionization are also discussed.The ionization probability and selectivity factors,as evaluation indexes,are difficult to improve synchronously by adjusting systematic parameters.Besides,the existence of metastable state may play a negative role when its population is low enough.

Chromosome-level genome and population genomics of the intermediate horseshoe bat(Rhinolophus affinis)reveal the molecular basis of virus tolerance in Rhinolophus and echolocation call frequency variation

Horseshoe bats(genus Rhinolophus,family Rhinolophidae)represent an important group within chiropteran phylogeny due to their distinctive traits,including constant high-frequency echolocation,rapid karyotype evolution,and unique immune system.Advances in evolutionary biology,supported by high-quality reference genomes and comprehensive whole-genome data,have significantly enhanced our understanding of species origins,speciation mechanisms,adaptive evolutionary processes,and phenotypic diversity.However,genomic research and understanding of the evolutionary patterns of Rhinolophus are severely constrained by limited data,with only a single published genome of R.ferrumequinum currently available.In this study,we constructed a high-quality chromosome-level reference genome for the intermediate horseshoe bat(R.affinis).Comparative genomic analyses revealed potential genetic characteristics associated with virus tolerance in Rhinolophidae.Notably,we observed expansions in several immune-related gene families and identified various genes functionally associated with the SARS-CoV-2 signaling pathway,DNA repair,and apoptosis,which displayed signs of rapid evolution.In addition,we observed an expansion of the major histocompatibility complex class II(MHC-II)region and a higher copy number of the HLA-DQB2 gene in horseshoe bats compared to other chiropteran species.Based on whole-genome resequencing and population genomic analyses,we identified multiple candidate loci(e.g.,GLI3)associated with variations in echolocation call frequency across R.affinis subspecies.This research not only expands our understanding of the genetic characteristics of the Rhinolophus genus but also establishes a valuable foundation for future research.

Comparative Analysis of Improving Effects of 12 Maize Populations with Improved S_1 Selection Method

ln this study, 12 maize populations were improved with the improved S1 selection method, aiming to increase the improvement efficiency of maize popula-tions. The results showed that number of rows per spike, number of grains per row and 100-grain weight were the three important component traits of maize yield. The highest genetic increment was found in Mengqun 2, fol owed by Mengqun 4, Mengqun 1 and other 7 maize populations. Negative genetic increment was shown in Mengqun 3 and 3 introduced foreign maize populations. Some changes were shown in spikes, plant traits and genetic diversity of maize populations. Based on our results, we concluded that Mengqun 2, Mengqun 4, Zhongzong 7, Mengqun C and Mengqun A could be directly used for the line breeding by selfing for their higher genetic increment of yield and better improvement effects of other agricultural traits. Compared with these 5 populations, the improvement potential of other maize populations was limited for their lower genetic increment.

Effects of Reciprocal Recurrent Selection on Grain Yield in Two Tropical-Temperate Maize Synthetic Populations Tuxpeño-Reid and Suwan-Lancaster

Reid, Lancaster, Tuxpeno and Suwan are the most common maize (Zea mays L.) germplasms. Reid × Lancaster and Suwan × Tuxpeno are very important heterotic patterns in temperate areas and tropical areas, respectively. Broadening the genetic basis of maize has usually been conducted in inter-populations formed by crossing temperate and tropical germplasms. Reciprocal recurrent selection (RRS) is a breeding procedure to improve the inter-populational cross of two base populations. The objective of this study was to evaluate the direct and indirect effects of reciprocal recurrent selection on grain yield in the TR (Tuxpeno-Reid) and SL (Suwan-Lancaster) maize populations. The populations and the inter-populational crosses of each selection cycle, as well as two commercial hybrids, were evaluated in four environments. The effect of mean grain yield on TR × SL inter-population crosses was 4.63% (or 0.365 Mg·ha-1) cycle-1. The grain yield of SL increased by 2.78% (or 0.20 Mg·ha-1) cycle-1, but the grain yield of TR essentially did not change. Most changes in other agronomic traits occurred in the desired direction. After 3 selection cycles, the ear tip-barrenness length decreased in TR × SL, TR and SL by 39.70%, 37.50% and 24.57%, respectively, which indicates that the increase in grain yield may be largely due to a decreasing ear tip-barrenness length. The mid-parent heterosis of grain yield of the inter-populational cross increased from 15.49% to 25.96% from C0 to C3. The mean grain yields of TRC3 × SLC3 were 100.01% and 103.88% of the mean grain yields of the commercial single-crosses GD8 and QD16, respectively. The results suggest that Tuxpeno-Reid × Suwan-Lancaster may be possible new heterotic patterns in the southern region of China.

A feature selection method combined with ridge regression and recursive feature elimination in quantitative analysis of laser induced breakdown spectroscopy

In the spectral analysis of laser-induced breakdown spectroscopy,abundant characteristic spectral lines and severe interference information exist simultaneously in the original spectral data.Here,a feature selection method called recursive feature elimination based on ridge regression(Ridge-RFE)for the original spectral data is recommended to make full use of the valid information of spectra.In the Ridge-RFE method,the absolute value of the ridge regression coefficient was used as a criterion to screen spectral characteristic,the feature with the absolute value of minimum weight in the input subset features was removed by recursive feature elimination(RFE),and the selected features were used as inputs of the partial least squares regression(PLS)model.The Ridge-RFE method based PLS model was used to measure the Fe,Si,Mg,Cu,Zn and Mn for 51 aluminum alloy samples,and the results showed that the root mean square error of prediction decreased greatly compared to the PLS model with full spectrum as input.The overall results demonstrate that the Ridge-RFE method is more efficient to extract the redundant features,make PLS model for better quantitative analysis results and improve model generalization ability.

Study on Quality Improvement Effect and Separate Character of Soybean Male Sterile (MS1) Recurrent Selection Population

To solve the problem that soybean has narrow genetic base, we constructed a series of male sterile recurrent selection populations, and studied the effects of quality improvement and practical value. An LD-base population, which fits to our ecology type was constructed by 6 years＇ gene enrichment through the introduction of new genes from 23 local varieties and recurrent selection. The LD-base populations were then improved by making crosses with high protein and high oil genotypes. As a result we obtained a high protein sub-population （db） and a high oil sub-population （gy）, For the db sub-population, the protein content is 1.18% higher than the base population, 22.38% of the individuals contain 45% or more of protein, which is 10.99% higher than the base population. For the gy sub-population, oil content is 0.24% higher than the base population. Individuals with oil content of 20% or more are 11.05% higher than the base population. The quantitative characters such as flowering date, mature date, pod habit, and hilum color, etc., all showed wide range of separation, and the segregation ratio approached balance. The c.v. of branch number of ms1 recurrent population （72.8%） is higher than general cross-population （57.3%）, and the c.v. of 100 seed weight of ms1 （18.1%） is higher than general cross population （16.5%）, the coefficient of variation of plant height, pods per plant, and seeds per pod were not significantly different. It was demonstrated in this paper that the quality character of ms 1 male sterile recurrent selection population was improved by adding new genes. And the segregation of other characters widened, making the populations suitable for the objective of soybean breeding. In this paper, we also discussed the breeding method, key technology, and selection effect of soybean ms 1 population.

Comparisons of Three Recurrent Selection Methods in the Improvement of Maize Populations

The maize population Csyn 4 was improved for three cycles with three recurrent selection methods MS1, MS1-HS, and MHSRRS in northern China. A total of 40 NC Ⅱ testcrosses were made by four testers with Csyn 4 and 10 improved populations, which were evaluated in four environments in the cropping season of 2005. Analysis of variance indicated a significant progress （P〈 0.05） in yield and other chief agronomic traits in the improved populations and testcrosses, demonstrating that the three recurrent selection methods were effective for increasing grain yield of testcrosses and improvement of general combining ability in maize population. The average grain yield increase of population Csyn 4 in MS1, MS1-HS, and MHSRRS recurrent selections was 266.7 kg ha^-1 （5.3%）, 288.0 kg ha^-1 （5.7%）, and 231.3 kg ha^-1 （4.6%） per cycle, while the grain yield of S 1 progeny of population for Csyn 4 was increased by 420.0 kg ha^-1 （10.9%）, 376.0 kg ha^-1 （9.8%）, and 414.7 kg ha^-1 （10.8%） per cycle in MS1, MS1-HS, and MHSRRS recurrent selections, respectively. Linear responses （b） in the MS1, MS1-HS, and MHSRRS recurrent selections were the same as the realized responses of the selection （G） for grain yield increase of Csyn 4 and S1 progeny of the populations. The grain yield of testcrosses increased by 3.3-5.2% on average per cycle. The value of heterosis did not display any differences amongst the different cycles of selections. The GCA for yield component traits of population Csyn 4 was improved significantly by means of three selection methods, whereas the GCA for plant height, ear height, days to silking, and days to pollen did not show significant increase in the recurrent selections. GCA for the number of tassel branches were decreased in the selections, while GCA for the number of plant leaves were increased, but the difference was not significant.

A New Population Initialization of Particle Swarm Optimization Method Based on PCA for Feature Selection

In many fields such as signal processing,machine learning,pattern recognition and data mining,it is common practice to process datasets containing huge numbers of features.In such cases,Feature Selection(FS)is often involved.Meanwhile,owing to their excellent global search ability,evolutionary computation techniques have been widely employed to the FS.So,as a powerful global search method and calculation fast than other EC algorithms,PSO can solve features selection problems well.However,when facing a large number of feature selection,the efficiency of PSO drops significantly.Therefore,plenty of works have been done to improve this situation.Besides,many studies have shown that an appropriate population initialization can effectively help to improve this problem.So,basing on PSO,this paper introduces a new feature selection method with filter-based population.The proposed algorithm uses Principal Component Analysis(PCA)to measure the importance of features first,then based on the sorted feature information,a population initialization method using the threshold selection and the mixed initialization is proposed.The experiments were performed on several datasets and compared to several other related algorithms.Experimental results show that the accuracy of PSO to solve feature selection problems is significantly improved after using proposed method.

Improved Harris Hawks Algorithm and Its Application in Feature Selection

This research focuses on improving the Harris’Hawks Optimization algorithm(HHO)by tackling several of its shortcomings,including insufficient population diversity,an imbalance in exploration vs.exploitation,and a lack of thorough exploitation depth.To tackle these shortcomings,it proposes enhancements from three distinct perspectives:an initialization technique for populations grounded in opposition-based learning,a strategy for updating escape energy factors to improve the equilibrium between exploitation and exploration,and a comprehensive exploitation approach that utilizes variable neighborhood search along with mutation operators.The effectiveness of the Improved Harris Hawks Optimization algorithm(IHHO)is assessed by comparing it to five leading algorithms across 23 benchmark test functions.Experimental findings indicate that the IHHO surpasses several contemporary algorithms its problem-solving capabilities.Additionally,this paper introduces a feature selection method leveraging the IHHO algorithm(IHHO-FS)to address challenges such as low efficiency in feature selection and high computational costs(time to find the optimal feature combination and model response time)associated with high-dimensional datasets.Comparative analyses between IHHO-FS and six other advanced feature selection methods are conducted across eight datasets.The results demonstrate that IHHO-FS significantly reduces the computational costs associated with classification models by lowering data dimensionality,while also enhancing the efficiency of feature selection.Furthermore,IHHO-FS shows strong competitiveness relative to numerous algorithms.

Comparison, Selection and Progeny Test of Natural Populations of White Birch (Betula platyphylla Suk.) in Northern China

[Objectives]This study was conducted to rationally and effectively use natural genetic resources of white birch(Betula platyphylla Suk.),and improve the scientific and technological content of improved varieties.[Methods]With the progeny of the white birch populations naturally distributed in northern China as objects,based on genetic effect analysis and comprehensive evaluation,the genetic variation,heritability and genetic gain of the growth characters in the progeny forest were systematically analyzed,by which populations or individuals with good growth vigor and strong stress resistance and adaptability were finally selected.[Results]There were extremely significant differences in the growth characters between the natural populations of white birch in northern China.The variation was the smallest in tree height,followed by crown width,and largest in DBH,and the average coefficients of variation were 20.56%,32.25%and 33.00%,respectively.The differences in characters between progeny of the same population were also extremely significant.The growth characters of white birch were more controlled by genes,and the genetic gains were larger.The heritability of tree height,DBH and crown width was 0.971,0.816 and 0.576,respectively,and the genetic gains were 15.97%,21.54%and 13.87%,respectively.[Conclusions]With the growth characters as the main evaluation indexes,taking various influencing factors into account,the Shanxi[SX]population,Hebei[HB]population and Liaoning[LN]population were selected to be excellent populations,and LN305,SX516 and HB403 were excellent individuals,which are advised to be widely used in multi-generation genetic improvement breeding.

Gametic selection in a doubled haploid population derived from anther culture of indica/japonica hybrid of Oryza Sativa L.

It is one of the key problems for application ofanther culture in hybrid breeding, geneticanalysis, and molecular mapping whether thedoubled haploid (DH) population derived fromanther culture of rice crosses represents a ran-dom array of the microspore population, i.e.whether gametic selection occurs in androgene-sis. A DH population including 132 lines de-

Recurrent Selection for Improving Quality Characters of Male Sterile Restorer Lines of Brassica napus

[Objective] This study aimed to improve the quality characters of the male sterile restorer lines of Brassica napus by recurrent selection. [Method] The dominant male sterile alleles were used as outcross medium to be transformed with the favourable genes from thirteen materials, and finally excellent restorer materials were bred by recurrent selection. After that, the genetic diversity, genetic gains, fatty acid chain length and unsaturarion ratios of the improved populations were analyzed. [Result] The genetic diversity and genetic gains were obviously improved by the recurrent selection. Nine materials whose oil content exceeding 50% and 14 materials whose protein content exceeding 30% were acquired, and crossed with sterile lines. The comparative experiment showed that there were 11 combinations whose oil content was obviously enhanced compared with the control. [Conclusion] Recurrent selection is an effective way to improve the quality characters of the objective pop- ulations and breed favourable male sterile restorer lines of B. napus.

Balancing selection shapes population differentiation of major histocompatibility complex genes in wild golden snub-nosed monkeys

Small and isolated populations face several intrinsic risks,such as genetic drift,inbreeding depression,and reduced gene fow.Thus,patterns of genetic diversity and differentiation have become an important focus of conservation genetics research.The golden snub-nosed monkey Rhinopithecus roxellana,an endangered species endemic to China,has experienced rapid reduction in population size and severe population fragmentation over the past few decades.We measured the patterns of genetic diversity and population differentiation using both neutral microsatellites and adaptive major histocompatibility complex(MHC)genes in 2 R.roxellana populations(DPY and GNG)distributed on the northern and southern slopes of the Qinling Mountains,respectively.Eight MHC-linked haplotypes formed by 5 DQA1 alleles,5 DQB1 alleles,5 DRB1 alleles,and 4 DRB2 alleles were detected in the 2 populations.The larger GNG population showed higher genetic variation for both MHC and microsatellites than the smaller DPY population,suggesting an effect of genetic drift on genetic variation.Genetic differentiation index(FST)outlier analyses,principal coordinate analysis(PCoA),and inferred population genetic structure showed lower genetic differentiation in the MHC variations than microsatellites,suggesting that pathogen-mediated balancing selection,rather than local adaptation,homogenized the MHC genes of both populations.This study indicates that both balancing selection and genetic drift may shape genetic variation and differentiation in small and fragmented populations.

Genetic Variation Assessed with Microsatellites in Mass Selection Lines of the Pacific Oyster (Crassostrea gigas) in China

Abstract Four successive mass selection lines of the Pacific oyster, Crassostrea gigas, selected for faster growth in breeding pro- grams in China were examined at ten polymorphic microsatellite loci to assess the level of allelic diversity and estimate the effective population size. These data were compared with those of their base population. The results showed that the genetic variation of the four generations were maintained at high levels with an average allelic richness of 18.8-20.6, and a mean expected heterozygosity of 0.902-0.921. They were not reduced compared with those of their base population. Estimated effective population sizes based on temporal variances in microsatellite frequencies were smaller to that of sex ratio-corrected broodstock count estimates. Using a rela- tively large number ofbroodstock and keeping an equal sex ratio in the broodstock each generation may have contributed to retaining the original genetic diversity and maintaining relatively large effective population size. The results obtained in this study showed that the genetic variation was not affected greatly by mass selection progress and high genetic variation still existed in the mass selection lines, suggesting that there is still potential for increasing the gains in future generations of C. gigas. The present study provided im- portant information for future genetic improvement by selective breeding, and for the design of suitable management guidelines for genetic breeding of C. gigas.

Comparisons of Growth and Survival Performance Among Selected Families and Wild Populations of Fenneropenaeus chinensis

In this study,families of selected population for growth(SP_BWT),selected population for white spot syndrome virus(WSSV)resistance(SP_RW),Bohai wild population(WP_BH)and Huanghai wild population(WP_HH)of F.chinensis were constructed through artificial insemination and with the standardized procedure of larvae rearing.Growth and survival performance were studied among four populations after a 70 days common test.The results showed that the maximum least square mean of body weight was 17.50 g in SP_BWT while the minimum was 13.03 g in WP_HH.Compared with WP_BH,body weight of SP_BWT increased by 23.41%(P<0.01)and that of SP_RW by 12.20%(P>0.05).Body weights of SP_BWT and SP_RW were significantly higher than that of WP_HH,which increased by 34.31%(P<0.01)and 22.10%(P<0.05),respectively.The mean AGR of four populations was 0.19,0.18,0.17 and 0.16 g d^(-1),respectively.Coefficient of variation of body weight among four populations was high,which ranged from 32.67% to 35.25%.Such a range showed that there was the potentiality for further improvement in selected populations.Coefficient of variation of survival rate among four populations was low,varying between 3.20% and 5.90%.The difference of survival was highly significant(P<0.01)between SP_BWT and WP_BH,and significant(P<0.05)between SP_RW and WP_BH.However,no significant difference among other populations(P>0.05)was observed.Different growth performances were also observed among different families in each population.The body weight of 798F family was the highest.The absolute growth rate(AGR)was 0.25 g d^(-1),150%higher than that of the lowest one,0.1 g d^(-1) in 807F family.Survival rate of families among four populations was different.The highest was 94.74%,and the lowest was 71.88%.

Effects of anthropogenic disturbances on natural regeneration and population structure of gum arabic tree (Acacia senegal)in the woodlands of Lake Baringo ecosystem, Kenya

Despite the ecological and economic importance of Acacia senegal, little is known about the effects of anthropogenic disturbances on its natural regeneration patterns and population structure. We investigated the effects of these factors within the Lake Baringo woodland ecosystem. Data was collected from 60 plots of 20 m × 20 m systematically distributed in four A. senegal-dominated populations within the Lake Baringo woodland. Sample populations spanned a degradation gradient measured by a population disturbance index (PDI). Trees were measured for diameter at breast height (DBH) and categorized by growth stages: seedling, sapling and adult tree. Higher seedling and sapling densities were recorded in lightly than heavily disturbed populations, but only sapling density was significantly different between the two disturbance levels (P = 0.02). Lightly disturbed populations revealed a reversed J-shape size-class distribution (SCD) indicative of stable structure unlike the heavily disturbed populations. The quotient and permutation indices indicated unstable populations with episodic recruitment and mortality. Our study reveals that natural regeneration and population structure of A. senegal were affected majorly by selective harvesting and heavy browsing. Suitable management strategies to control livestock grazing and illegal tree harvesting within the woodland is required to promote conservation of the species genetic resources

Development of Genome-Wide Scan for Selection Signature in Farm Animals

Identifying targets of positive selection in farm animals has, until recently, been frustratingly slow, relying on the analysis of individual candidate genes. Genomics, however, has provided the necessary resources to systematically interrogate the entire genome for signatures of selection. This review described important recent results derived from the application of genome-wide scan to the study of genetic changes in farm animals. These included findings of regions of the genome that showed breed differentiation, evidence of selective sweeps within individual genomes and signatures of demographic events. Particular attention is focused on the study of the implications for domestication. To date, sixteen genome-wide scans for recent or ongoing positive selection have been performed in farm animals. A key challenge is to begin synthesizing these newly constructed maps of selection into a coherent narrative of animal breed evolutionary history and derive a deeper mechanistic understanding of how animal populations improve or evolve. The major insights from the surveyed studies are highlighted and directions for future study are suggested.

Highly selective population of two excited states in nonresonant two-photon absorption

A nonresonant two-photon absorption process can be manipulated by tailoring the ultra-short laser pulse. In this paper, we theoretically demonstrate a highly selective population of two excited states in the nonresonant two- photon absorption process by rationally designing a spectral phase distribution. Our results show that one excited state is maximally populated while the other state population is widely tunable from zero to the maximum value. We believe that the theoretical results may play an important role in the selective population of a more complex nonlinear process comprising nonresonant two-photon absorption, such as resonance-mediated （2-~l）-three-photon absorption and （2q-1）-resonant multiphoton ionization.

Family tree and population: Distinction and similarity of the analysis on example of hemophilia

On the basis of Hardy-Weinberg law the distinction in the philosophy of the description of a family tree and a population is considered. With the help of introduction of the equivalent constant mutagen factor both in a family tree and in a population, the analysis of hemophilia is led. Influence of selection at presence of hemophilia is considered. On the basis of idea of Danforth and Haldane about the balance mutagenesis and selection at presence of hemophilia, the inter-relation of selection parameter and the equivalent constant mutagen factor is found. It is shown, that dynamics of development of hemophilia in a family tree and in population are similar.