Is Fisher's model necessary for the theory of population improvement?

Summary It is shown here that genetic advance in one cycle of recurrent selection can be formulated directly in terms of covariances between relatives by application of the general statistical principle of linear prediction. For practical use of such formulae it is necessary to estimate the corresponding covariance between relatives from the mating design used. With General Combining Ability selection such estimation is direct. For other types of selection, it is necessary to derive associated covariances from other types of covariances but it is not necessary to use classical results of covariances between relatives in terms of genetic effects. Indeed, covariances can be derived without factorial decomposition of the genetic effects at one locus, i.e., without the concept of additivity and dominance. This approach allows a simple derivation of the genetic advance after n cycles of selection, followed by m generations of intercrossing, with a minimum of assumptions.     

The choice of selection index in kale (Brassica oleracea L.) population improvement

Summary The use of selection indices was explored in a kale (Brassica oleracea L. var. acephala) breeding programme aimed at increasing digestible organicmatter (DOM) yield, and lowering S-methyl cysteine sulphoxide (SMCO) and thiocyanate ion (SCN^–) contents by half-sib family selection. The predicted overall response with the optimum index (1.59) was slightly better than with the base index (1.56) which in turn was superior to the desired gains index (1.41). All three indices were expected to increase height and reduce amino acid content, mainly because of genetical correlations between DOM yield and height (r=0.76) and between SMCO and amino acid contents (r=0.81). Elimination of these correlated responses with the desired gains index would result in virtually no progress, and with the restricted index an undesirable increase in SMCO content would occur.     

Bias in the prediction of genetic gain due to mass and half-sib selection in random mating populations

The prediction of gains from selection allows the comparison of breeding methods and selection strategies, although these estimates may be biased. The objective of this study was to investigate the extent of such bias in predicting genetic gain. For this, we simulated 10 cycles of a hypothetical breeding program that involved seven traits, three population classes, three experimental conditions and two breeding methods (mass and half-sib selection). Each combination of trait, population, heritability, method and cycle was repeated 10 times. The predicted gains were biased, even when the genetic parameters were estimated without error. Gain from selection in both genders is twice the gain from selection in a single gender only in the absence of dominance. The use of genotypic variance or broad sense heritability in the predictions represented an additional source of bias. Predictions based on additive variance and narrow sense heritability were equivalent, as were predictions based on genotypic variance and broad sense heritability. The predictions based on mass and family selection were suitable for comparing selection strategies, whereas those based on selection within progenies showed the largest bias and lower association with the realized gain.     

Genomics reveals new landscapes for crop improvement

The sequencing of large and complex genomes of crop species, facilitated by new sequencing technologies and bioinformatic approaches, has provided new opportunities for crop improvement. Current challenges include understanding how genetic variation translates into phenotypic performance in the field.     

Doubled haploids for estimating genetic variances and a scheme for population improvement in self-pollinating crops

Summary An analysis is derived for a diallel experiment in which each cross is represented by a number of homozygous Unes developed by the doubled haploid method. Both additive and additive x additive genetic variances can be estimated with this analysis. A population-improvement scheme involving the doubled haploid or single seed descent methods is also proposed.     

Integrating genomic selection into dairy cattle breeding programmes: a review

Extensive genetic progress has been achieved in dairy cattle populations on many traits of economic importance because of efficient breeding programmes. Success of these programmes has relied on progeny testing of the best young males to accurately assess their genetic merit and hence their potential for breeding. Over the last few years, the integration of dense genomic information into statistical tools used to make selection decisions, commonly referred to as genomic selection, has enabled gains in predicting accuracy of breeding values for young animals without own performance. The possibility to select animals at an early stage allows defining new breeding strategies aimed at boosting genetic progress while reducing costs. The first objective of this article was to review methods used to model and optimize breeding schemes integrating genomic selection and to discuss their relative advantages and limitations. The second objective was to summarize the main results and perspectives on the use of genomic selection in practical breeding schemes, on the basis of the example of dairy cattle populations. Two main designs of breeding programmes integrating genomic selection were studied in dairy cattle. Genomic selection can be used either for pre-selecting males to be progeny tested or for selecting males to be used as active sires in the population. The first option produces moderate genetic gains without changing the structure of breeding programmes. The second option leads to large genetic gains, up to double those of conventional schemes because of a major reduction in the mean generation interval, but it requires greater changes in breeding programme structure. The literature suggests that genomic selection becomes more attractive when it is coupled with embryo transfer technologies to further increase selection intensity on the dam-to-sire pathway. The use of genomic information also offers new opportunities to improve preservation of genetic variation. However, recent simulation studies have shown that putting constraints on genomic inbreeding rates for defining optimal contributions of breeding animals could significantly reduce achievable genetic gain. Finally, the article summarizes the potential of genomic selection to include new traits in the breeding goal to meet societal demands regarding animal health and environmental efficiency in animal production.     

Plant biotechnology for crop improvement

The typical crop improvement cycle takes 10–15 years to complete and includes germplasm manipulations, genotype selection and stabilization, variety testing, variety increase, proprietary protection and crop production stages. Plant tissue culture and genetic engineering procedures that form the basis of plant biotechnology can contribute to most of these crop improvement stages. This review provides an overview of the opportunities presented by the integration of plant biotechnology into plant improvement efforts and raises some of the societal issues that need to be considered in their application.     

水稻轮回选择群体XTBG-HP1表型遗传多样性分析

该研究基于4个陆稻群体及172个水稻品种或杂交组合,构建了水稻多亲本隐性核不育轮回选择群体XTBG-HP1,并经过4次轮回重组,采用16个表型性状对其进行了遗传多样性分析。结果表明:(1)该群体14个数量性状符合正态分布,各表型均存在极端性状个体。(2)数量性状变异系数范围为0.08～0.41,均值为0.20; Shannon-Wiener多样性指数范围为0.72～1.92,均值为1.50。(3)群体在株型与产量构成因子性状方面有显著的相关性,对株型的选择可以实现产量性状的改良。(4)剑叶长、每穗粒总数、千粒重、穗长、粒长、一次枝梗数、有效穗数、剑叶宽、二次枝梗数、抽穗期10个性状可作为群体综合评价指标。(5)剑叶长、二次枝梗数、每穗粒总数3个表型性状具有较高的遗传变异、丰富的遗传多样性及与综合得分F值相关系数较高。综合以上结果发现,后期群体进行基因挖掘、品种改良以及优良育种材料的选育可以基于剑叶长、二次枝梗数及每穗粒总数3个表型性状,同时要充分利用群体株型与产量构成因子性状间的显著相关性。此外,该研究群体中极端单性状或综合得分F值较高的个体,可进一步用于品种选育。     

Plant genetic engineering for crop improvement

Plant genetic engineering has long since left its experimental stage: transgenic plants with resistance to viruses, bacteria, fungi, various pests and abiotic stresses have already been released in their hundreds. Transgenic plants can produce better fruits and food of higher quality than wild-types, and can be used as bioreactors for the synthesis of pharmaceutically important compounds. This review portrays some of the achievements in this field of plant molecular biology.The authors are with Plant Molecular Biology, Biozentrum, Frankfurt University, Marie-Curie-Strasse 9, D-60439 Frankfurt, Germany     

Genetic improvement for phosphorus efficiency in soybean: a radical approach

Background

Low phosphorus (P) availability is a major constraint to soybean growth and production. Developing P-efficient soybean varieties that can efficiently utilize native P and added P in the soils would be a sustainable and economical approach to soybean production.

Scope

This review summarizes the possible mechanisms for P efficiency and genetic strategies to improve P efficiency in soybean with examples from several case studies. It also highlights potential obstacles and depicts future perspectives in ‘root breeding’.

Conclusions

This review provides new insights into the mechanisms of P efficiency and breeding strategies for this trait in soybean. Root biology is a new frontier of plant biology. Substantial efforts are now focusing on increasing soybean P efficiency through ‘root breeding’. To advance this area, additional collaborations between plant breeders and physiologists, as well as applied and theoretical research are needed to develop more soybean varieties with enhanced P efficiency through root modification, which might contribute to reduced use of P fertilizers, expanding agriculture on low-P soils, and achieving more sustainable agriculture.     

Genetic variation for growth and selection in adult plants of Eucalyptus badjensis

The aim of this study was to evaluate Eucalyptus badjensis concerning the genetic variation for growth traits and the potential of the species in supporting a breeding programme. The field trial was a provenance/progeny test established in Campina da Alegria, Santa Catarina, Brazil (latitude 26°52′05.1″ S, longitude 51°48′47.5″ W, altitude 1,015 m) in a soil classified as Latossolic Alumino-Ferric Brown Nitosol. The experiment comprised 60 open-pollinated progenies from the provenances Glenbog and Badja State Forest, New South Wales, Australia. Ten replicates and plots with six plants in row were used. At the age of 17 years, 279 trees were assessed for diameter of the bole at breast height (DBH), total tree height (H) and volume of wood with bark (Vol). After submitting the data to statistical genetic analysis, the overall means for DBH, H and Vol were 45.17 cm, 33.30 m and 2.84 m³, and the estimates of additive coefficient of variation [CV^a(%)] were 12.59%, 5.91% and 26.51%, respectively. Heritability coefficients of additive effects (h^a2) were also estimated and the following values were found: 0.443, 0.312 and 0.358. Thirty-nine trees from 25 different progenies were selected. The expected means of the provenances after improvement were 50.02 cm, 34.35 m and 3.47 m³ for DBH, H and Vol, respectively.     

Intergeneric somatic hybrid plants from sexually incompatible woody species: Citrus sinensis and Severinia disticha

Summary The fusion of Citrus sinensis cv. Hamlin (sweet orange) protoplasts isolated from an embryogenic suspension culture with Severinia disticha (Philippine box orange) protoplasts isolated from epicotyl-derived callus with organogenic potential, resulted in the regeneration of allotetraploid somatic hybrid plants. Plant regeneration was a function of complementation, combining the capacity for somatic embryogenesis of C. sinensis with the organogenic ability of S. disticha. Confirmation of somatic hybrid identity was based on leaf morphology, chromosome number, and analyses of phosphoglucose mutase (PGM) and malate dehydrogenase (MDH) zymograms. Hybrid plants were multiplied organogenically and exhibited morphology intermediate to that of the parents. This is the first example of somatic hybrid plants produced between sexually incompatible woody genera.Florida Agricultural Experiment Station Journal Series No. 8198     

Marker assisted selection for the improvement of two antagonistic traits under mixed inheritance

A Monte Carlo simulation was used to investigate the potential of Marker Assisted Selection (MAS) in a multiple-trait situation. Only additive effects were considered. The base population was assumed to be in linkage equilibrium and, next, the population was managed over 15 discrete generations, 10 males and 50 females were chosen out of the 100 candidates of each sex. Performance for two traits was simulated with an overall heritability of a given trait equal to 0.25 or 0.10 and the overall genetic correlation between traits was generally equal to -0.4 except in one case where it was equal to 0. The model involved one biallelic QTL, accounting for 10 or 20% of the genetic variance of a given trait, plus polygenes. Initial allelic frequencies at the QTL were generally equal to 0.5 but in one case were equal to 0.1 and 0.9. A marker with 120 different alleles in the 60 founder parents was simulated in the vicinity of the QTL. Two values of the recombination rate between these two loci were considered, 0.10 and 0.02. The genetic evaluation was based on a multiple-trait BLUP animal model, accounting (MAS) or not (conventional BLUP) for marker information. Two sets of simulations were run: (1) a "missing data"case, with males having no record for one of the traits, and (2) a "secondary trait"case, with one trait having a weight in the aggregate genotype 4 times less than the other trait and the QTL acting only on this secondary trait. In the first set, evaluation methods were found to mainly affect the accuracy of overall genetic values prediction for the trait with missing data. In comparison with BLUP, MAS led to an extra overall genetic response for the trait with missing data, which was strongly penalised under the conventional BLUP, and to a deficit in response for the other trait. This more balanced evolution of the two traits was obtained, however, at the expense of the long-term overall cumulated response for the aggregate genotype, which was 1 to 2.5% lower than the one obtained under the conventional BLUP. In the second set of simulation, in the case of low initial frequency (0.1) of the QTL allele favourable to the secondary trait, MAS was found to be substantially more efficient to avoid losing this allele than BLUP only when the QTL had a large effect and the marker was close. More benefits should be expected from MAS with more specific applications, such as early selection of animals, or by applying dynamic procedures i.e. letting the respective weights to QTL and polygenic values in the selection criterion vary across generation.     

Optimal mass selection policies for schemes with overlapping generations and restricted inbreeding

Optimum breeding schemes for maximising the rate of genetic progress with a restriction on the rate of inbreeding (per year or per generation) are investigated for populations with overlapping generations undergoing mass selection. The optimisation is for the numbers of males and females to be selected and for their distribution over age classes. Expected rates of genetic progress (ΔG) are combined with expected rates of inbreeding (ΔF) in a linear objective function (Φ = ΔG - λΔF) which is maximised. A simulated annealing algorithm is used to obtain the solutions. The restriction on inbreeding is achieved by increasing the number of parents and, in small schemes with severe restrictions, by increasing the generation interval. In the latter case the optimum strategy for obtaining the maximum genetic gain is far from truncation selection across age classes. In most situations, the optimum mating ratio is one but the differences in genetic gain obtained with different mating ratios are small. Optimisation of schemes when restricting the rate of inbreeding per generation leads to shorter generation intervals than optimisation when restricting the rate of inbreeding per year.     

Mating schemes for optimum contribution selection with constrained rates of inbreeding

The effect of non-random mating on genetic response was compared for populations with discrete generations. Mating followed a selection step where the average coancestry of selected animals was constrained, while genetic response was maximised. Minimum coancestry (MC), Minimum coancestry with a maximum of one offspring per mating pair (MC1) and Minimum variance of the relationships of offspring (MVRO) mating schemes resulted in a delay in inbreeding of about two generations compared with Random, Random factorial and Compensatory mating. In these breeding schemes where selection constrains the rate of inbreeding, ΔF, the improved family structure due to non-random mating increased genetic response. For schemes with ΔF constrained to 1.0% and 100 selection candidates, genetic response was 22% higher for the MC1 and MVRO schemes compared with Random mating schemes. For schemes with a less stringent constraint on ΔF or more selection candidates, the superiority of the MC1 and MVRO schemes was smaller (5–6%). In general, MC1 seemed to be the preferred mating method, since it almost always yielded the highest genetic response. MC1 mainly achieved these high genetic responses by avoiding extreme relationships among the offspring, i.e. fullsib offspring are avoided, and by making the contributions of ancestors to offspring more equal by mating least related animals.     

Genetic improvement of a parasitoid: Response of Trioxys pallidus to laboratory selection with azinphosmethyl

Colonies of Trioxys pallidus Haliday (Hymenoptera: Aphidiidae) were collected from California walnut orchards during 1985–86 and screened for variability of responses to azinphosmethyl. Variability was found and laboratory selection was initiated with four colonies. All colonies responded to selection; after seven to 12 selections, three colonies were combined (Select colony) and selection was conducted an additional 27 times. The corresponding base colonies were also combined and maintained for comparisons (Base). Concentration/mortality lines obtained for the Select and Base colonies after five and 27 selections indicated seven‐ and 9.2‐fold differences in LC₅₀ values respectively. Survival of the resistant strain varied with bioassay method and decreased in the order: clip cages on treated foliage > treated plastic cups with untreated mesh tops > treated plastic cups with treated mesh tops> treated cups with treated solid lids. The initial bioassay results with treated plastic cups suggested that the selection response was inadequate to allow the resistant strain to survive field rats of azinphosmethyl. When the resistant strain's survival was evaluated with bioassay methods more closely mimicking field conditions (clip cages on field‐treated foliage), we concluded the selected strain could survive field rates of azinphosmethyl.     

A method of line development using doubled haploids: the single doubled haploid descent recurrent selection

Summary Different methods of line development using doubled haploids in recurrent selection are presented. They are divided into two types: recurrent selection with progeny testing and recurrent selection on the phenotype of lines. It is shown that one of the best methods of line development is based on single doubled haploid descent recurrent selection. Only one line is studied per plant of the population, and the best lines are intercrossed. Using this method it is very easy to extract lines for variety development.     

基因组选择及其应用

品种选育在农业生产中占有十分重要的地位,育种值估计是品种选育的核心。随着遗传标记的发展,尤其是高通量的基因分型技术,使得从基因组水平估计育种值成为可能,即基因组选择。文章将基因组选择的方法分为两类:一是基于估计等位基因效应来预测基因组估计育种值(GEBV),如最小二乘法,随机回归-最佳线性无偏预测(RR-BLUP)、Bayes、主成分分析等方法;二是基于遗传关系矩阵来预测GEBV,通过采用高通量标记构建个体间的遗传关系矩阵,然后用线性混合模型来预测育种值,即GBLUP法,并以这两种分类简要介绍了基因组选择各种方法的大致原理。影响基因组选择准确性的因素主要有标记类型和密度、单倍型长度、参考群体大小和标记-数量性状基因座(QTL)连锁不平衡(LD)大小等;在基因组选择的各种方法中,一般说来Bayes方法和GBLUP方法具有较高的准确性,最小二乘法最差;GBLUP计算速度快,能够将标记和系谱结合起来,因而比其他方法更具优势。尽管基因组选择取得了很大进展,但在理论方面还面临着一些挑战,如联合育种、长期选择的遗传进展及如何解析与性状有关和无关的标记等。基因组选择在一些动植物育种上已经开始应用,在人类遗传倾向预测和进化动力学研究中也有潜在的应用前景。基因组选择在个体间亲缘关系的量化上有了突破,比传统方法更加精确,因此,基因组选择将会是动植物育种史上革命性的事件。     

Mating animals by minimising the covariance between ancestral contributions generates less inbreeding without compromising genetic gain in breeding schemes with truncation selection

We reasoned that mating animals by minimising the covariance between ancestral contributions (MCAC mating) will generate less inbreeding and at least as much genetic gain as minimum-coancestry mating in breeding schemes where the animals are truncation-selected. We tested this hypothesis by stochastic simulation and compared the mating criteria in hierarchical and factorial breeding schemes, where the animals were selected based on breeding values predicted by animal-model BLUP. Random mating was included as a reference-mating criterion. We found that MCAC mating generated 4% to 8% less inbreeding than minimum-coancestry mating in the hierarchical and factorial breeding schemes without any loss in genetic gain. Moreover, it generated upto 28% less inbreeding and about 3% more genetic gain than random mating. The benefits of MCAC mating over minimum-coancestry mating are worthwhile because they can be achieved without extra costs or practical constraints. MCAC mating merely uses pedigree information to pair the animals more appropriately and is clearly a worthy alternative to minimum-coancestry mating and probably any other mating criterion. We believe, therefore, that MCAC mating should be used in breeding schemes where pedigree information is available.