Simulation of gene pyramiding in Drosophila melanogaster

Gene pyramiding has been successfully practiced in plant breeding for developing new breeds or lines in which favorable genes from several different lines were integrated.But it has not been used in animal breeding,and some theoretical investigation and simulation analysis with respect to its strategies,feasibility and efficiency are needed before it can be implemented in animals.In this study,we used four different pure fines of Drosophila melanogaster,each of which is homozygous at a specific mutant gene with a visible effect on phenotype,to simulate the gene pyramiding process and analyze the duration and population size required in different pyramiding strategies.We finally got the ideal individuals,which are homozygous at the four target genes simultaneously.This study demonstrates that gene pyramiding is feasible in animal breeding and the interaction between genes may affect the final results.     

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.     

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.     

Improving salinity tolerance of plants through conventional breeding and genetic engineering: An analytical comparison

The last century has witnessed a substantial improvement in yield potential, quality and disease resistance in crops. This was indeed the outcome of conventional breeding, which was achieved with little or no knowledge of underlying physiological and biochemical phenomena related to a trait. Also the resources utilized on programs involving conventional breeding were not of great magnitude. Plant breeders have also been successful during the last century in producing a few salt-tolerant cultivars/lines of some potential crops through conventional breeding, but this again has utilized modest resources. However, this approach seems now inefficient due to a number of reasons, and alternatively, genetic engineering for improving crop salt tolerance is being actively followed these days by the plant scientists, world-over. A large number of transgenic lines with enhanced salt tolerance of different crops can be deciphered from the literature but up to now only a very few field-tested cultivars/lines are known despite the fact that considerable resources have been expended on the sophisticated protocols employed for generating such transgenics. This review analytically compares the achievements made so far in terms of producing salt-tolerant lines/cultivars through conventional breeding or genetic engineering.     

Evaluating genetic relationships between tropical maize inbred lines by means of AFLP profiling

Diversity among tropical maize inbred lines that compose breeding programs, is not well known. The lack of this information has made the arrangement of heterotic groups to be used for breeding purposes difficult. Methods of molecular analysis have been used as efficient alternatives for evaluating genetic diversity, aiming at heterotic group arrangement and acquisition of new hybrids. In this study, AFLP (amplified fragment length polymorphism) was used to investigate the genetic relationships among 96 tropical maize inbred lines from two different origins. The polymorphism level among the genotypes and the possibility of their allocation in heterotic groups were evaluated. Besides, correlations among genetic diversity and flowering time were analyzed. Nine primer combinations were used to obtain AFLP markers, producing 638 bands, 569 of which were polymorphic. Genetic similarities (GS), determined by Jaccard's similarity coefficient, varied from 0.345 to 0.891, with an average of 0.543. The dendrogram based on the GS and on the UPGMA cluster method did not separate the inbred lines in well-defined groups. Aiming at separating the lines into more accurate groups, Tocher's optimization procedure was carried out, 17 groups being identified. Association between flowering time and germplasm pools was detected. AFLP showed itself to be a robust assay, revealing a great power of detection of genetic variability in the tropical germplasm, and also demonstrated to be very useful for guiding breeding programs.     

Inducing drought tolerance in plants: Recent advances

Undoubtedly, drought is one of the prime abiotic stresses in the world. Crop yield losses due to drought stress are considerable. Although a variety of approaches have been used to alleviate the problem of drought, plant breeding, either conventional breeding or genetic engineering, seems to be an efficient and economic means of tailoring crops to enable them to grow successfully in drought-prone environments. During the last century, although plant breeders have made ample progress through conventional breeding in developing drought tolerant lines/cultivars of some selected crops, the approach is, in fact, highly time-consuming and labor- and cost-intensive. Alternatively, marker-assisted breeding (MAB) is a more efficient approach, which identifies the usefulness of thousands of genomic regions of a crop under stress conditions, which was, in reality, previously not possible. Quantitative trait loci (QTL) for drought tolerance have been identified for a variety of traits in different crops. With the development of comprehensive molecular linkage maps, marker-assisted selection procedures have led to pyramiding desirable traits to achieve improvements in crop drought tolerance. However, the accuracy and preciseness in QTL identification are problematic. Furthermore, significant genetic × environment interaction, large number of genes encoding yield, and use of wrong mapping populations, have all harmed programs involved in mapping of QTL for high growth and yield under water limited conditions. Under such circumstances, a transgenic approach to the problem seems more convincing and practicable, and it is being pursued vigorously to improve qualitative and quantitative traits including tolerance to biotic and abiotic stresses in different crops. Rapid advance in knowledge on genomics and proteomics will certainly be beneficial to fine-tune the molecular breeding and transformation approaches so as to achieve a significant progress in crop improvement in future. Knowledge of gene regulation and signal transduction to generate drought tolerant crop cultivars/lines has been discussed in the present review. In addition, the advantages and disadvantages as well as future prospects of each breeding approach have also been discussed.     

Hybridization and selection for improving seed protein in barley

Summary Hybridization followed by continuous selection of lines of barley from different cross-combinations involving high protein-high lysine genotypes and the agronomically superior strains resulted in breaking the negative correlations between 1000 grain weight and high protein content and high DBC values. The methodology of DBC-Kjeldahl protein adopted in the present study is likely to be useful in identifying high lysine lines. The present study has shown considerable variability with respect to protein content and grain weight and has provided interesting genotypes which can be used in synthesising lines with improved nutritional quality and productivity in barley. The success in breaking the undesirable linkages to factors that impair the endosperm development is due to sufficient genetic variability in the initial breeding material as well as the use of suitable breeding procedures like the full-sib mating in the early segregating generations.     

SOMACLONAL AND GAMETOCLONAL VARIATION

For several years it has been recognized that introduction of plant cells into culture results in genetic changes. These genetic alterations have been recovered in the plants regenerated from cell cultures. More recently it has been recognized that this method of introducing genetic changes into crop plants could be used to develop new breeding lines. The technology of introducing genetic variation by using cell culture has been termed somaclonal and gametoclonal variation. This paper reviews the history of this technology and offers genetic documentation of somaclonal variation in tomato. As this variation represents a new tool for the plant breeder, breeding strategies for the use of this variation are presented and discussed. Somaclonal and gametoclonal variation are new tools for the geneticist and plant breeder that permit reduction in the time period for new variety development and that permit access to new classes of genetic variation.     

Identification of a third haplotype of the sequence linked to the Restorer-of-fertility (Rf) gene and its implications for male-sterility phenotypes in peppers (Capsicum annuum L.)

Cytoplasmic male sterility (CMS), one of the most important traits in crop breeding, has been used for commercial seed production by F1 hybrid cultivars of pepper (Capsicum annuum L.). To develop reliable molecular markers for allelic selection of the Restorer-of-fertility (Rf) gene, which is known to be a major determinant of pollen fertility restoration in peppers, a sequence of approximately 10 kb flanking an RAPD fragment closely linked to the Rf locus was obtained by genome walking. A homology search revealed that this sequence contained an LTR retrotransposon and a non-LTR LINE-like retrotransposon. Sequencing of this Rf-linked region to search for polymorphisms between a dominant and recessive allele revealed 98% nucleotide sequence identity between them. A third polymorphic haplotype of the Rf-linked sequence, which has 94-96% nucleotide sequence identity with the two previously isolated haplotypes, was identified among a large number of breeding lines. Utilizing polymorphic sequences in the haplotypes, PCR markers were developed for selection of particular haplotypes and used to examine the distribution of the haplotypes in diverse breeding lines, cultivars, and C. annuum germplasms. Surprisingly, the third haplotype was the predominant type in C. annuum germplasms, while its frequency in F1 hybrid cultivars was relatively low. Meanwhile, analysis of breeding lines whose Rf allele genotypes and male-sterility phenotypes were already known revealed that the third haplotype was mainly present in exotic breeding lines that cause unstable male-sterility when combined with sterile cytoplasms.     

Assessment of the agronomic value of QTL on chromosomes 2H and 4H linked to tolerance to boron toxicity in barley (Hordeum vulgare L.)

Improved boron (B) tolerance has been an objective of barley breeding programs in regions where B toxicity occurs. Traits associated with B tolerance have been mapped on chromosomes 2H and 4H and it has been proposed that these be used for marker assisted selection for B tolerance. However, there has been little or no improvement in yield using this strategy. This study examined the reasons for the small yield differences among different lines of barley that differ in B tolerance. Experiments used backcross lines derived from crosses between the B-tolerant landrace Sahara 3771 and two adapted recurrent parents, Sloop and VB9104. Lines with different combinations of the Sahara 3771 alleles on chromosomes 2H and 4H were grown over three growing seasons at sites where barley is prone to B toxicity. Grain yields of the backcross lines were similar to or lower than those of the recurrent parents despite showing differences in the expression of B toxicity symptoms and in B concentration in vegetative tissue. There were few significant differences in grain yield among the backcross lines. Variation in dry matter production among the backcross lines in each of the three growing seasons was unrelated to shoot B concentrations while grain yield was correlated with shoot B concentration only among the backcross lines of VB9104 in one season. In this case the yield loss was 4% per 10 mg kg^-1 increase in shoot B concentration. Variation in shoot B concentration and yield across seasons was much greater than that observed among the different barley lines. Reduced B accumulation was associated with higher shoot sodium concentration among the Sloop backcross lines. The results suggest that yield gains from selection based largely on B exclusion and symptoms expression may be small and strongly affected by site and seasonal effects. In the regions where other soil constraints, such as soil salinity and micronutrient deficiencies are also important, reducing B uptake alone may have little effect on yield if these other soil properties are also limiting yields.     

主要农作物细胞质雄性不育系育性恢复基因研究进展

提升作物产量、抗逆性和品质的主要手段之一是利用杂种优势,其中细胞质雄性不育/恢复(CMS/Rf)系统是应用最广的雄性不育系统。研究细胞质雄性不育系育性恢复机理是“三系”法选育的重要分子遗传学基础。目前,各个作物已经创制了不同类型的不育系。随着分子技术、基因组学和测序技术的深入,大量育性恢复基因已被定位,且部分已被克隆和功能鉴定。针对主要作物中恢复基因的遗传模式,分子标记定位、克隆及CMS/Rf系统在杂交育种中的应用进行了系统总结。希望本文能为今后恢复系分子标记辅助选育,或利用转基因、基因编辑手段创制新恢复系提供思路。     

Assessing genetic identity of sporophytic offspring of the brown alga Undaria pinnatifida derived from mono‐crossing of gametophyte clones by use of amplified fragment length polymorphism and microsatellite markers

The haploid stage of gametophytes of the subtidal brown alga Undaria pinnatifida can be vegetatively propagated under favorable conditions. This unique characteristic makes it possible to establish independent gametophyte cell lines that are zoospore‐derived. Sporophytic offspring can be generated through hybridizing the male and female gametophytes, which are derived from different cell lines. Accumulated experiences in this and other species in Laminariales demonstrated the applicability of this novel way to breed desired strains for open‐sea cultivation. Sporophytic offspring originated from mono‐crossing of male and female gametophyte clones were shown to have similar morphological characteristics under identical ambient conditions. However, there has been no report to relate this similarity on molecular levels. In this report, amplified fragment length polymorphism (AFLP) and microsatellite markers were used to analyze the genetic identity of sporophytic offspring of U. pinnatifida originated from two mono‐crossing lines (M1 and M2), two self‐breeding lines (S1 and S2) and one wild population (W). Totally 318 AFLP loci were revealed by use of 11 primer sets, of which 4.7%, 0.3%, 17.9%, 16.4% and 36.5% were polymorphic in M1, M2, S1, S2 and W, respectively. The pairwise genetic identity among the individuals of the same line was assessed. It was shown that offspring from mono‐crossing lines had a higher degree of identity (95.6–100%) than self‐breeding lines (87.7–98.4%) and the wild population (81.5–92.1%). Analysis by use of six microsatellite loci also revealed a higher genetic identity among individuals of the mono‐crossing line, further confirming the results of AFLP analysis. Results from this investigation support, on molecular levels, the novel way to produce and maintain strains in U. pinnatifida by use of different gametophyte cell lines.     

The B.T.O. in the Seventies

Since the cessation of grazing and the reduction of Rabbit activity the chalk downland at the eastern end of the Chiltern Hills has been invaded by scrub, mainly hawthorn, which has attracted a uniquely diverse breeding bird community. Census studies show how different species are adapting to the various phases of the secondary succession towards woodland climax, and some broad lines of management are indicated.     

中国禾谷类作物野生近缘植物在育种中的利用

中国主要禾谷类作物有水稻、小麦、大麦、燕麦、玉米、高粱、粟、黍稷,它们的野生近缘植物在中国禾谷类作物育种中得到了较好的利用,不仅拓宽了作物的遗传基础,而且培育出优良品种在生产上大面积推广,在提高粮食产量中起到了重要作用.     

我国不同年代玉米自交系茎秆性状演替规律

茎秆是玉米植株重要的组成部分,与植株倒伏、籽粒产量密切相关.研究我国玉米茎秆性状变化趋势,探讨不同年代茎秆性状演变规律,为我国玉米抗倒伏及高产品种选育提供参考.本研究以20世纪60-90年代65个代表性玉米自交系为材料,调查植株茎高、穗位高、茎节数、穗位节、茎粗、茎秆含水量、茎秆含糖量7个茎秆性状,及其衍生的穗位系数(...     

Ribosomal DNA as a convenient probe to follow segregation and possible divergency from expected homozygosity after haploidization of an androgenetic process

Summary Restriction fragment length polymorphism of the wheat nuclear ribosomal DNA has been studied in several steps of a breeding scheme, including parental genotypes, F1 hybrid, F9 generation, and anther-derived doubled haploid lines obtained from F9. Ribosomal DNA represents a suitable molecular marker in following segregation and possible divergency from expected homozygosity after haploidization of an androgenetic process. It has been shown to undergo variations among the first cycle-doubled haploid lines in the relative amount of two different sizes of ribosomal DNA repeat units. The specificity and peculiar properties of the plant system used allowed us to assign an intrachromosomal location (short arm of the chromosomes 1B, 1R or 6B) to several ribosomal DNA repeat units that differ by the length of their nontranscribed spacer region.     

Identification and mapping of net form of net blotch resistance in South African barley

Net form of net blotch (NFNB) caused by the fungus Pyrenophora teres f. teres is an economically important foliar disease of barley (Hordeum vulgare) in southern and eastern Africa. Little attention has been given to disease resistance breeding, and knowledge about the presence of NFNB resistance in breeding lines is limited. Deploying resistance into varieties used in this region is important for future control of the disease. We have identified NFNB disease resistance in existing South African breeders’ lines and have mapped the resistance in line UVC8. Six different trials, three conducted in South Africa and another three in Australia, were used to identify resistance QTL. A major QTL was identified on chromosome 6H having a LOD score of 40.5 and 55% of the phenotypic variance explained. Kompetitive Allele Specific PCR (KASP?) markers were designed for this QTL region. These and microsatellite markers can now be used to routinely select for NFNB resistance.     

DSLET (D-ser2-leu5-enkephalin-Thr6) produces analgesia on the hot plate by mechanisms largely different from DAGO and morphine-like opioids

Fifteen generations of selective breeding were used to produce lines (strains) of mice which differ markedly from one another in levorphanol-induced antinociception on the hot plate assay. These are the high antinociceptive response (HAR) and low antinociceptive response (LAR) selection lines, which now differ by over 5-fold in the i.p. dose of levorphanol doubling control (no drug or saline) latency scores. We sought to determine if these large genetically-mediated differences in antinociceptive sensitivity bred into these selection lines with i.p. levorphanol would generalize equally to a series of enkephalin analogues known to differ in their selectivity for mu and delta opioid receptors. DAGO (D-ala2, MePhe4, Gly-ol5 enkephalin), a highly mu selective agent, produced a 67-fold difference between HAR and LAR mice in the slopes of the dose-response curves on the hot plate assay, while DSLET (D-ser2, leu enkephalin Thr6), a delta selective agent, only produced a 5.4-fold difference via the i.c.v. route. DADLE (D-ala, D-ser enkephalin) a slightly delta preferring ligand, was found to be intermediate (17.4-fold difference). These findings demonstrate that selective breeding has been quite successful in altering those genes which control analgesia due to mu selective agents, while relatively little change has occurred in those genes which control analgesia due to delta agonists. Thus, analgesia mediated by the former has been genetically dissociated from analgesia mediated by the latter, implying that DAGO has mechanisms of action largely dependent of DSLET on the hot plate assay. These findings are consistent with the contention that the mu receptor mediates analgesia produced by DAGO, while a different receptor (presumably delta) mediates much of the analgesic effects of DSLET.     

Effect of population size and unbalanced data sets on QTL detection using genome-wide association mapping in barley breeding germplasm

Over the past two decades many quantitative trait loci (QTL) have been detected; however, very few have been incorporated into breeding programs. The recent development of genome-wide association studies (GWAS) in plants provides the opportunity to detect QTL in germplasm collections such as unstructured populations from breeding programs. The overall goal of the barley Coordinated Agricultural Project was to conduct GWAS with the intent to couple QTL detection and breeding. The basic idea is that breeding programs generate a vast amount of phenotypic data and combined with cheap genotyping it should be possible to use GWAS to detect QTL that would be immediately accessible and used by breeding programs. There are several constraints to using breeding program-derived phenotype data for conducting GWAS namely: limited population size and unbalanced data sets. We chose the highly heritable trait heading date to study these two variables. We examined 766 spring barley breeding lines (panel #1) grown in balanced trials and a subset of 384 spring barley breeding lines (panel #2) grown in balanced and unbalanced trials. In panel #1, we detected three major QTL for heading date that have been detected in previous bi-parental mapping studies. Simulation studies showed that population sizes greater than 384 individuals are required to consistently detect QTL. We also showed that unbalanced data sets from panel #2 can be used to detect the three major QTL. However, unbalanced data sets resulted in an increase in the false-positive rate. Interestingly, one-step analysis performed better than two-step analysis in reducing the false-positive rate. The results of this work show that it is possible to use phenotypic data from breeding programs to detect QTL, but that careful consideration of population size and experimental design are required.     

应用RNAi技术培育抗TMV病毒转基因烟草

利用烟草花叶病毒(TMV)外壳蛋白基因构建RNAi干涉载体, 通过叶盘法转化至烟草K326 和龙江911两个栽培品种。对转基因株系的荧光定量PCR分析表明, 不同转基因株系的病毒RNA靶序列都得到一定程度的降解, 抗病性鉴定结果证实, 转基因K326和龙江911两个栽培品种的转基因材料分别有83％和90％转基因株系对TMV呈现免疫级抗性。