Genetics of qualitative traits in domesticated chia (Salvia hispanica L.)

In Salvia hispanica L., several changes in qualitative characters, including seed coat color, stem pigmentation, and shattering, have evolved with cultivation and domestication. Three F(2) segregating generations from crosses between wild and domesticated parents were scored for three qualitative traits. A single recessive gene, designated scc, was found to govern the white seed characteristic. A single dominant gene, designated SSP, was found to control striated stem pigmentation. A complete dominance of open calyx over closed calyx was observed in F(1) generations and small numbers of plants with closed calyxes were observed in F(2) generations, not conforming to Mendelian ratios. For this non-shattering trait, a complementation test was conducted between two lines representative of geographically and morphologically divergent domesticated varieties. Complementary gene action was not observed in any F(1) plants, and all F(2) plants were homogeneous with respect to the trait, suggesting the same genetic control for non-shattering among domesticated varieties. An analysis of limited data for linkage of SSP and scc indicated that the two loci segregate independently.     

水稻耐淹涝性状的遗传分析和SSR标记的研究

淹涝胁迫对水稻生产造成了严重影响, 发掘可应用于耐淹涝辅助选择的分子标记(MAS), 将有助于水稻耐淹涝性状的遗传改良。应用耐淹涝材料FR13A和淹涝敏感材料IR39595-503-2-1-2为亲本做正反交获得F₁和F₂代群体。对正反交的F₁群体的耐淹涝性状进行遗传分析, 发现正反交的F₁代群体在耐淹涝性状上没有显著差异, 说明耐淹涝性状是核基因控制。从两次淹涝处理中F₂代群体的分离情况来看, 来源于FR13A的耐淹特性表现出数量-质量性状遗传的特点。当淹涝胁迫压力比较轻时表现为数量性状遗传, 具有微效多基因的作用。当淹涝胁迫压力增大时, 表现为主效基因控制的质量性状。在SSR分析中, 187对SSR引物中有73对引物在两亲本间有明显的差异, 差异率为39%。用这73对差异引物, 对F2群体进行多态筛选, 结果筛选到一个与耐淹涝性状连锁的标记RM219, 验证了耐淹涝性状确实由主效基因Sub1控制, 因此, RM219在水稻耐淹涝育种中具有利用价值。     

Inheritance of growth habit detected by genetic linkage analysis using microsatellites in the common bean (Phaseolus vulgaris L.)

The genetic linkage map for the common bean (Phaseolus vulgaris L.) is a valuable tool for breeding programs. Breeders provide new cultivars that meet the requirements of farmers and consumers, such as seed color, seed size, maturity, and growth habit. A genetic study was conducted to examine the genetics behind certain qualitative traits. Growth habit is usually described as a recessive trait inherited by a single gene, and there is no consensus about the position of the locus. The aim of this study was to develop a new genetic linkage map using genic and genomic microsatellite markers and three morphological traits: growth habit, flower color, and pod tip shape. A mapping population consisting of 380 recombinant F10 lines was generated from IAC-UNA × CAL143. A total of 871 microsatellites were screened for polymorphisms among the parents, and a linkage map was obtained with 198 mapped microsatellites. The total map length was 1865.9 cM, and the average distance between markers was 9.4 cM. Flower color and pod tip shape were mapped and segregated at Mendelian ratios, as expected. The segregation ratio and linkage data analyses indicated that the determinacy growth habit was inherited as two independent and dominant genes, and a genetic model is proposed for this trait.     

Mapping of qualitative and quantitative phenotypic traits in <Emphasis Type="Italic">Rosa</Emphasis> using AFLP markers

A segregating population of 91 hybrids issued from a cross between a dihaploid rose, derived from the haploidisation of a modern cultivar, and a diploid species was used to construct linkage maps of the parental genomes. As in other recent genetic studies in Rosa, AFLPs were used as molecular markers. Two segregating qualitative traits, recurrent blooming and double corolla, already known to be inherited as single recessive and dominant genes, respectively, were recorded in the mapping population. A quantitative trait, thorn density of the shoots, was also evaluated in this population. Sixty eight and 108 AFLP markers located on 8 and 6 linkage groups could be analysed in the female and male parent, respectively. The two recorded qualitative phenotypic markers were mapped as well as the quantitative one, after having performed QTL analyses on the parental maps in the latter case. It appears that thorn quantity is controlled by a major and a minor QTL which are located on the same linkage group at 36.5 and 3.2 cM from the single seasonal-blooming gene, respectively.     

Overdominant epistatic loci are the primary genetic basis of inbreeding depression and heterosis in rice. II. Grain yield components

The genetic basis underlying inbreeding depression and heterosis for three grain yield components of rice was investigated in five interrelated mapping populations using a complete RFLP linkage map, replicated phenotyping, and the mixed model approach. The populations included 254 F(10) recombinant inbred lines (RILs) derived from a cross between Lemont (japonica) and Teqing (indica), two backcross (BC) and two testcross populations derived from crosses between the RILs and the parents plus two testers (Zhong413 and IR64). For the yield components, the RILs showed significant inbreeding depression and hybrid breakdown, and the BC and testcross populations showed high levels of heterosis. The average performance of the BC or testcross hybrids was largely determined by heterosis. The inbreeding depression values of individual RILs were negatively associated with the heterosis measurements of the BC or testcross hybrids. We identified many epistatic QTL pairs and a few main-effect QTL responsible for >65% of the phenotypic variation of the yield components in each of the populations. Most epistasis occurred between complementary loci, suggesting that grain yield components were associated more with multilocus genotypes than with specific alleles at individual loci. Overdominance was also an important property of most loci associated with heterosis, particularly for panicles per plant and grains per panicle. Two independent groups of genes appeared to affect grain weight: one showing primarily nonadditive gene action explained 62.1% of the heterotic variation of the trait, and the other exhibiting only additive gene action accounted for 28.1% of the total trait variation of the F(1) mean values. We found no evidence suggesting that pseudo-overdominance from the repulsive linkage of completely or partially dominant QTL for yield components resulted in the overdominant QTL for grain yield. Pronounced overdominance resulting from epistasis expressed by multilocus genotypes appeared to explain the long-standing dilemma of how inbreeding depression could arise from overdominant genes.     

Frameshift Suppression in SACCHAROMYCES CEREVISIAE VI. Complete Genetic Map of Twenty-Five Suppressor Genes

Five previously unmapped frameshift suppressor genes have been located on the yeast genetic map. In addition, we have further characterized the map positions of two suppressors whose approximate locations were determined in an earlier study. These results represent the completion of genetic mapping studies on all 25 of the known frameshift suppressor genes in yeast.—The approximate location of each suppressor gene was initially determined through the use of a set of mapping strains containing 61 signal markers distributed throughout the yeast genome. Standard meiotic linkage was assayed in crosses between strains carrying the suppressors and the mapping strains. Subsequent to these approximate linkage determinations, each suppressor gene was more precisely located in multi-point crosses. The implications of these mapping results for the genomic distribution of frameshift suppressor genes, which include both glycine and proline tRNA genes, are discussed.     

Genetic mapping of horizontal stripes in Lake Victoria cichlid fishes: benefits and pitfalls of using RAD markers for dense linkage mapping

The genetic dissection of naturally occurring phenotypes sheds light on many fundamental and longstanding questions in speciation and adaptation and is a central research topic in evolutionary biology. Until recently, forward‐genetic approaches were virtually impossible to apply to nonmodel organisms, but the development of next‐generation sequencing techniques eases this difficulty. Here, we use the ddRAD‐seq method to map a colour trait with a known adaptive function in cichlid fishes, well‐known textbook examples for rapid rates of speciation and astonishing phenotypic diversification. A suite of phenotypic key innovations is related to speciation and adaptation in cichlids, among which body coloration features prominently. The focal trait of this study, horizontal stripes, evolved in parallel in several cichlid radiations and is associated with piscivorous foraging behaviour. We conducted interspecific crosses between Haplochromis sauvagei and H. nyererei and constructed a linkage map with 867 SNP markers distributed on 22 linkage groups and total size of 1130.63 cM. Lateral stripes are inherited as a Mendelian trait and map to a single genomic interval that harbours a paralog of a gene with known function in stripe patterning. Dorsolateral and mid‐lateral stripes were always coinherited and are thus under the same genetic control. Additionally, we directly quantify the genotyping error rates in RAD markers and offer guidelines for identifying and dealing with errors. Uncritical marker selection was found to severely impact linkage map construction. Fortunately, by applying appropriate quality control steps, a genotyping accuracy of >99.9% can be reached, thus allowing for efficient linkage mapping of evolutionarily relevant traits.     

Genetics of tassel branch number in maize and its implications for a selection program for small tassel size

Summary Tassel branch numbers of six crosses of maize (Zea mays L.) were analyzed to determine inheritance of this trait. Generation mean analyses were used to estimate genetic effects, and additive and nonadditive components of variance were calculated and evaluated for bias due to linkage. Both narrow-sense and broad-sense heritabilities were estimated. Additive genetic variance estimates were significant in five of the six crosses, whereas estimates of variance due to nonadditive components were significant in only three crosses. Additionally, estimates of additive variance components usually were larger than corresponding nonadditive components. There was no evidence for linkage bias in these estimates. Estimates of additive genetic effects were significant in four of six crosses, but significant dominance, additive × additive and additive × dominance effects also were detected. Additive, dominance, and epistatic gene action, therefore, all influenced the inheritance of tassel branch number, but additive gene action was most important. Both narrow-sense and broadsense heritability estimates were larger than those reported for other physiological traits of maize and corroborated conclusions concerning the importance of additive gene action inferred from analyses of genetic effects and variances. We concluded that selection for smalltasseled inbreds could be accomplished most easily through a mass-selection and/or pedigree-selection system. Production of a small-tasseled hybrid would require crossing of two small-tasseled inbreds. We proposed two genetic models to explain unexpected results obtained for two crosses. One model involved five interacting loci and the other employed two loci displaying only additive and additive × additive gene action.Journal Paper No. J-9231 of the Iowa Agriculture and Home Economics Experiment Station, Ames, Iowa 50011. Project No. 2152     

A complex of serine protease genes expressed preferentially in cytotoxic T-lymphocytes is closely linked to the T-cell receptor alpha- and delta-chain genes on mouse chromosome 14

A complex of genes encoding serine proteases that are preferentially expressed in cytotoxic T-cells was shown to be closely linked to the T-cell receptor alpha- and delta-chain genes on mouse chromosome 14. A striking difference in recombination frequencies among linkage crosses was reported. Two genes, Np-1 and Tcra, which fail to recombine in crosses involving conventional strains of mice, were shown to recombine readily in interspecific crosses involving Mus spretus. This difference in recombination frequency suggests chromosomal rearrangements that suppress recombination in conventional crosses, recombination hot spots in interspecific crosses, or selection against recombinant haplotypes during development of recombinant inbred strains. Finally, a mutation called disorganization, which is located near the serine protease complex, is of considerable interest because it causes an extraordinarily wide variety of congenital defects. Because of the involvement of serine protease loci in several homeotic mutations in Drosophila, disorganization must be considered a candidate for a mutation in a serine protease-encoding gene.     

Genetic linkage mapping of multiple epiphyseal dysplasia to the pericentromeric region of chromosome 19.

Multiple epiphyseal dysplasia (MED) is an inherited chondrodystrophy that results in deformity of articular surfaces and in subsequent degenerative joint disease. The disease is inherited as an autosomal dominant trait with high penetrance. An MED mutation has been mapped by genetic linkage analysis of DNA polymorphisms in a single large pedigree. Close linkage of MED to 130 tested chromosomal markers was ruled out by discordant inheritance patterns. However, strong evidence for linkage of MED to markers in the pericentromeric region of chromosome 19 was obtained. The most closely linked marker was D19S215, with a maximum LOD score of 6.37 at theta = .05. Multipoint linkage analysis indicated that MED is located between D19S212 and D19S215, a map interval of 1.7 cM. Discovery of the map location of MED in this family will facilitate identification of the mutant gene. The closely linked DNA polymorphisms will also provide the means to determine whether other inherited chondrodystrophies have underlying defects in the same gene.     

Autosomal recessive inheritance of airway hyperreactivity to 5-hydroxytryptamine

We have previously reported that airway hyperresponsiveness to acetylcholine (ACh) is inherited as an autosomal recessive trait in A/J and C3H/HeJ mice and the progeny of crosses between them (FASEB J. 2: 2605-2608, 1988). In the present report, we have extended these studies by evaluating the biological variability in the airway response to 5-hydroxytryptamine (5-HT) and ACh among multiple genetically standardized inbred strains of mice. The pattern of airway responsiveness to ACh differed significantly from that of 5-HT in nine inbred strains of mice. A/J mice showed nonspecific airway hyperresponsiveness to both 5-HT and ACh. DBA/2J mice were hyperresponsive to 5-HT but not to ACh. An airway phenotype that resembled these inbred strains is termed HYPERREACTIVE. The C3H/HeJ and C57BL/6J inbred strains were minimally reactive to either ACh or 5-HT. Airway phenotypes that resembled these minimally reactive strains are termed HYPOREACTIVE. The frequency of HYPERRACTIVE and HYPOREACTIVE offspring from crosses between A/J and C3H/HeJ mice or DBA/2J and C57BL/6J mice is consistent with a single autosomal recessive gene, primarily determining airway hyperresponsiveness to 5-HT. We report linkage studies which suggest that these genes are not closely linked and that 5-HT and ACh airway hyperresponsiveness is inherited independently. The results of these studies suggest that murine nonspecific airway hyperresponsiveness is determined by multiple genes.     

Analysis of quantitative trait loci using hybrid pedigrees: quantitative traits of animals

A method is proposed for analysis of quantitative traits in animal hybrid pedigrees formed by crosses between outbred lines differing in allele frequencies of the genes controlling the trait studied. The method is based on the decomposition of trait variances into components and uses maximization of the likelihood function for estimating model parameters, which allows the estimation of additive and dominance effects of the gene involved in trait determination and its allele frequencies, as well as determination of the chromosomal position of this gene relative to genotyped markers. To test the linkage of this gene with markers, a statistic with the noncentral chi(2) distribution has been chosen. Analytical expressions for the power of this method have been derived. The method has been tested on small model hybrid pedigrees. Phenotypic values of the trait and information on marker genotypes for each individual in hybrid pedigrees are original data for the analysis of a quantitative trait.     

Genetic analysis of floral anthocyanin pigmentation traits in Asiatic hybrid lily using molecular linkage maps

To understand the genetic background of two floral anthocyanin pigmentation traits, anthocyanin pigmentation in the flower tepals and spot formation, in the Asiatic hybrid lily (2n = 24), segregation of the two traits among 96 F₁ plants derived from a cross between commercial cultivars 'Montreux' and 'Connecticut King' were investigated. 'Montreux' has anthocyanin pigmentation in the tepals with many spots, and 'Connecticut King' has flowers with carotenoid pigmentation without spots. The F₁ plants with or without anthocyanin pigment in the tepals segregated with a 1:1 segregation ratio, indicating that a single gene controls anthocyanin pigmentation in the tepals. The number of spots per square centimeter of all tepals showed continuous distribution in the F₁ plants. To map the loci for the two anthocyanin pigmentation traits, molecular linkage maps in the Asiatic hybrid lily were constructed using a double pseudo-testcross strategy, with the same F₁ plants used for phenotypic evaluation, and 212 PCR-based DNA markers. The trait for anthocyanin pigmentation in tepals was used as a trait marker. The map of 'Montreux' comprised 95 markers in 26 linkage groups, and the map of 'Connecticut King' used 119 markers in 24 linkage groups. The total map lengths were 867.5 and 1,114.8 cM, respectively. The trait locus for anthocyanin pigmentation in the tepals was between markers ASR35-180 and P506-40 in linkage group 1 of the 'Montreux' map with a map distance of 1.2 cM and 2.6 cM, respectively. A single-point analysis of quantitative trait loci (QTLs) for tepal spot number identified two putative QTLs in linkage groups 1 and 19 of the 'Connecticut King' map. One putative QTL in linkage group 19 explained 64% of the total phenotypic variation. Because both putative QTLs were mapped on the linkage map of 'Connecticut King' that has no spots, dominant alleles of them might suppress spot formation.     

Genetics of dietary obesity in AKR/JxSWR/J mice: segregation of the trait and identification of a linked locus on Chromosome 4

We describe a new multiple gene mouse model of differential sensitivity to dietary obesity that provides a tool for dissecting the genetic basis for body composition and obesity. AKR/J and SWR/J male mice, as well as male progeny of intercrosses between these strains, were fed a high-fat diet for 12 weeks beginning at 5 weeks of age. Body weight and energy intake were assessed weekly. At the conclusion of the dietary manipulation, an adiposity index was calculated by dividing the weight of seven dissected adipose depots by the carcass weight. AKR/J mice had approximately sixfold greater adiposity than SWR/J mice. Examination of the segregation of the adiposity trait in the progeny of crosses between these strains indicates that the trait is determined by a minimum of one to four genetic loci and that there is significant dominance of the AKR/J genotype. A preliminary analysis with markers linked to the known mouse obesity genes ob, db, tub, and fat showed no linkage with these loci. However, a quantitative trait locus was found that maps distal to the db gene on Chromosome (Chr) 4. This locus has been designated dietary obese 1 or Do1.     

Genetic analysis of ecological relevant morphological variability in Plantago lanceolata L.

Summary Morphological variability was analysed in an F₂-generation derived from crosses between two ecotypes of Plantago lanceolata L. Six allozyme loci, localised in five linkage groups, were used as markers. For two marker loci, Got-2 and Gpi-1, segregations did not fit monogenic ratios. In the linkage groups to which these two loci belonged, male sterility genes appeared to be present. In these crosses, male sterility (type 3, as described by Van Damme 1983) may be determined by two recessive loci located in the linkage groups of Got-2 and of Gpi-1. Many correlations of morphological and life history characters with allozyme markers were observed. The quantitative trait loci did not appear to be concentrated in major gene complexes. Often many loci were involved, sometimes with effects opposite to those expected from the population values. Main effects of the linkage groups appeared to be more important than interaction effects in determining variability. It also appeared that there is a positive correlation between the number of heterozygous allozyme loci and generative growth.Grassland Species Research Group Publication No. 115     

新疆肉羊18号染色体上与后臀肌发育相关基因的多态性分析

通过对新疆肉羊18号染色体与后臀肌发育相关基因的多态性分析,试图找到与新疆肉羊后臀肌性状发达相关基因,为肉羊分子标记辅助选择提供理论线索。运用PCR-SSCP、PCR-RFLP方法,对陶赛特和萨福克两个肉羊品种群体及其与本地细毛羊杂交1代和2代群体Callipyge（CLPG）基因的多态性进行分析,结果表明：位于18号染色体内的DLK1和GTL2间的103849 bp处没有发现PCR-RFLP多态性,表明新疆肉羊后臀肌过度发育与CLPG基因无关。随后,实验进一步对18号染色体Meg3.9位点158520处进行PCR-SSCP分析,发现扩增片段存在着多态性;Meg3.9扩增片段多态性位点在肉羊群体中的基因型有AA、AB和AC,以AA型为主。其中AA、AB基因型与新疆肉羊后臀肌肉发达的表型无关（P>0.05）,AC基因型与新疆肉羊后臀肌肉发达的表型相关（P<0.05）。在陶赛特与本地细毛羊杂交1代群体中,AC基因型的屠体重和屠宰率与AA、AB基因型差异显著（P<0.05）,但三种基因型的各月龄体重没有差异(P>0.05)。通过以上分析可以推断,引起新疆肉用绵羊后臀肌过度发育的性状不是CLPG基因内9571-268.3位点突变导致,可能还存在其他基因或与其连锁的多个QTL的共同作用。     

A score test for the linkage analysis of qualitative and quantitative traits based on identity by descent data from sib-pairs

We propose a general likelihood-based approach to the linkage analysis of qualitative and quantitative traits using identity by descent (IBD) data from sib-pairs. We consider the likelihood of IBD data conditional on phenotypes and test the null hypothesis of no linkage between a marker locus and a gene influencing the trait using a score test in the recombination fraction theta between the two loci. This method unifies the linkage analysis of qualitative and quantitative traits into a single inferential framework, yielding a simple and intuitive test statistic. Conditioning on phenotypes avoids unrealistic random sampling assumptions and allows sib-pairs from differing ascertainment mechanisms to be incorporated into a single likelihood analysis. In particular, it allows the selection of sib-pairs based on their trait values and the analysis of only those pairs having the most informative phenotypes. The score test is based on the full likelihood, i.e. the likelihood based on all phenotype data rather than just differences of sib-pair phenotypes. Considering only phenotype differences, as in Haseman and Elston (1972) and Kruglyak and Lander (1995), may result in important losses in power. The linkage score test is derived under general genetic models for the trait, which may include multiple unlinked genes. Population genetic assumptions, such as random mating or linkage equilibrium at the trait loci, are not required. This score test is thus particularly promising for the analysis of complex human traits. The score statistic readily extends to accommodate incomplete IBD data at the test locus, by using the hidden Markov model implemented in the programs MAPMAKER/SIBS and GENEHUNTER (Kruglyak and Lander, 1995; Kruglyak et al., 1996). Preliminary simulation studies indicate that the linkage score test generally matches or outperforms the Haseman-Elston test, the largest gains in power being for selected samples of sib-pairs with extreme phenotypes.     

Genetic analysis ofCochliobolus heterostrophus polyoxin-resistant mutants

Nine polyoxin-resistant mutants ofCochliobolus heterostrophus were isolated after ethyl methanesulphonate mutagenesis. All were highly resistant to polyoxin (MIC≥1,600 ppm). Crosses between the mutants and a wild-type strain revealed that the resistance trait was inherited to the offsprings in different fashions. Four of the mutant strains inherited polyoxin resistance in a 1∶1 segregation ratio, indicating that the phenotypes in these strains were due to alteration at a single locus. Allelism tests revealed four new loci,Pol1, Pol2, Pol3 andPol4, for polyoxin resistance in these mutant strains. The genes responsible for the phenotypes of the other five mutant strains were not determined, because of extremely slow growth of progenies in one cross, sterility in another cross, and inexplicable responses to polyoxin of the progenies in the other crosses. No linkage was detected between the genes for polyoxin resistance and mating type.     

Sensitized polygenic trait analysis

Genetic variation in many biological processes and evolutionary adaptations is caused by polygenes – genes that act in combination to affect a particular trait. Despite the recent identification of several polygenes, many remain to be found, suggesting that new experimental and analytical methods are needed to facilitate their discovery. Here we discuss sensitized polygenetic trait analysis, a method that has emerged recently for simplifying the genetic analysis of polygenic traits. The method uses a known single gene mutation in linkage testing crosses to ‘sensitize’ the analysis. By increasing the frequency of affected individuals in segregating populations, linkages are more readily detected. This method has considerable potential, especially given the increasing variety of mutations that can be used to sensitize the genetic analysis of polygenic traits.