Comparative genetic mapping between duplicated segments on maize chromosomes 3 and 8 and homoeologous regions in sorghum and sugarcane

Comparative mapping within maize, sorghum and sugarcane has previously revealed the existence of syntenic regions between the crops. In the present study, mapping on the sorghum genome of a set of probes previously located on the maize and sugarcane maps allow a detailed analysis of the relationship between maize chromosomes 3 and 8 and sorghum and sugarcane homoeologous regions. Of 49 loci revealed by 46 (4 sugarcane and 42 maize) polymorphic probes in sorghum, 42 were linked and were assigned to linkage groups G (28), E (10) and I (4). On the basis of common probes, a complete co-linearity is observed between sorghum linkage group G and the two sugarcane linkage groups II and III. The comparison between the consensus sorghum/sugarcane map (G/II/III) and the maps of maize chromosomes 3 and 8 reveals a series of linkage blocks within which gene orders are conserved. These blocks are interspersed with non-homoeologous regions corresponding to the central part of the two maize chromosomes and have been reshuffled, resulting in several inversions in maize compared to sorghum and sugarcane. The results emphasize the fact that duplication will considerably complicate precise comparative mapping at the whole genome scale between maize and other Poaceae.     

Comparison of bread wheat lines selected by doubled haploid, single-seed descent and pedigree selection methods

 Yield performance of each group of ten spring bread wheat lines selected by doubled haploid (DH), single-seed descent (SSD) and pedigree selection (PS) methods from three F₁ crosses was compared with the aim of evaluating the DH method in breeding programs. Populations of 65–97 DH lines and 110 SSD lines per cross were used for selection. PS lines were developed by repeated selections from 1500 F₂ plants. Yield evaluation was performed at the F₆ generation of SSD and PS lines along with DH lines in a 2-year field experiment. It took only 2 years from the planting of wheat materials for DH production to the planting of selected DH lines for yield evaluation. There was no significant difference in grain yield between DH lines and PS lines selected from an F₁ cross whose parental varieties were closely related in their pedigrees. In two crosses with low coefficients of parentage and a large variation in their progenies, grain yield of selected DH lines was significantly lower than those of selected SSD and PS lines. These results confirm that the DH method can save time in obtaining recombinant inbred lines ready for yield evaluation. However, a larger DH population is required to achieve the same level of genetic advance with the PS method in crosses containing greater genetic variation. Received: 23 December 1997 / Accepted: 12 March 1998     

Transmission of important chromosomal regions under selection revealed in rice pedigree breeding programs

Genetic analysis across a whole plant genome based on pedigree information offers considerable potential for enhancing genetic gain from plant breeding programs through quantitative trait loci (QTL) mapping and marker-assisted selection. Here, we report its application for graphically genotyping varieties used in Chinese japonica rice (Oryza sativa L.) pedigree breeding programs. We identified 34 important chromosomal regions from the founder parent that are under selection in the breeding programs, and by comparing donor genomic regions that are under selection with QTL locations of agronomic traits, we found that QTL clustered in important genomic regions, in accordance with association analyses of natural populations and other previous studies. The convergence of genomic regions under selection with QTL locations suggests that donor genomic regions harboring key genes/QTL for important agronomic traits have been selected by plant breeders since the 1950s from the founder rice plants. The results provide better understanding of the effects of selection in breeding programs on the traits of rice cultivars. They also provide potentially valuable information for enhancing rice breeding programs through screening candidate parents for targeted molecular markers, improving crop yield potential and identifying suitable genetic material for use in future breeding programs.     

Identification of genomic regions affecting plant height in sorghum and maize

The objective of this study was to use restriction fragment length polymorphisms (RFLPs) to determine the genetic location and effects of genomic regions controlling plant height in sorghum. F₂ plants (152) from the cross CK60 x PI229828 were used. Genomic and cDNA clones (106) identified 111 loci distributed among ten linkage groups covering 1299 cM. Interval mapping identified four regions, each in a separate linkage group. These regions may correspond to loci (dw) previously identified by alleles with qualitative effects. Also, these regions identified in sorghum may be orthologous to those previously reported for plant height in maize. Gene effects and gene action varied among genomic regions. In each region, PI229828 alleles resulted in increased plant height. Each region accounted for 9.2–28.7% of the phenotypic variation. Positive, additive effects ranged from 15 to 32cm. Tallness was dominant or overdominant and conferred by alleles from PI229828 for three quantitative trait loci (QTL). At the fourth QTL, PI229828 contributed to increased plant height, but short stature was partially dominant. One digenic interaction was significant. The presence of a PI229828 allele at one region diminished the effects of the other region. A multiple model indicated that these four regions collectively accounted for 63.4% of the total phenotypic variation. The utility of this information for germplasm conversion through backcross breeding is discussed.Journal Paper No. J. 15649 of the Iowa Agriculture and Home Economic Experiment Station, Ames, Iowa. Project No. 3134     

A direct comparison between the genetic maps of sorghum and rice

A direct comparison of the genetic linkage maps of sorghum and rice is proposed. It is based on the mapping of a common set of 123 RFLP probes scattered on the genomes of both species. For each species a composite map was established by merging two individual maps comprising many common loci. This enabled us to confirm the global correspondence scheme that had previously been established between the chromosomes of sorghum and rice. It also provided a more detailed insight into the conservation of synteny and colinearity: 69% of the loci mapped on a given rice chromosome mapped to the corresponding homoeologous chromosome in sorghum; among them, 84% formed a colinear arrangement between the two species. Local inversions and translocations were detected. Received: 27 April 2000 / Accepted: 26 May 2000     

Group coancestry-controlled selection in a Pinus sylvestris L. breeding program

 Integer Linear Programming was used to maximize genetic gain from selection at a given level of relatedness. Variances and breeding values for total height were available for 296 plus-trees of Pinus sylvestris which had been evaluated by open-pollinated progeny testing at a single test site in northern Sweden. Second-generation breeding and selection scenarios for this breeding population were evaluated using simulated data derived deterministically from normal distributions of estimated breeding values of progeny around mid-parent family means. The study considered two mating designs, assortative and non-assortative single-pair mating, and two selection criteria, individual phenotype and performance of half-sib progeny. Relatedness (group coancestry) was restricted to a level equivalent to that given by within-family selection of 2 trees per family from each of 25 families (the current standard in Sweden). Selection that allows the best-performing families to contribute a greater number of progeny was superior, both when the breeding population size was limited to 50 individuals and when it was allowed to be larger. The selected set giving the greatest average breeding value under restricted group coancestry included the best individual from families that would have been rejected under application of standard within-family selection. We made a comparison of the present value on retrieved gain between phenotypic selection and evaluation by progeny testing. Received: 24 November 1998 / Accepted: 14 December 1998     

The power comparison of the haplotype-based collapsing tests and the variant-based collapsing tests for detecting rare variants in pedigrees

Background

Both common and rare genetic variants have been shown to contribute to the etiology of complex diseases. Recent genome-wide association studies (GWAS) have successfully investigated how common variants contribute to the genetic factors associated with common human diseases. However, understanding the impact of rare variants, which are abundant in the human population (one in every 17 bases), remains challenging. A number of statistical tests have been developed to analyze collapsed rare variants identified by association tests. Here, we propose a haplotype-based approach. This work inspired by an existing statistical framework of the pedigree disequilibrium test (PDT), which uses genetic data to assess the effects of variants in general pedigrees. We aim to compare the performance between the haplotype-based approach and the rare variant-based approach for detecting rare causal variants in pedigrees.

Results

Extensive simulations in the sequencing setting were carried out to evaluate and compare the haplotype-based approach with the rare variant methods that drew on a more conventional collapsing strategy. As assessed through a variety of scenarios, the haplotype-based pedigree tests had enhanced statistical power compared with the rare variants based pedigree tests when the disease of interest was mainly caused by rare haplotypes (with multiple rare alleles), and vice versa when disease was caused by rare variants acting independently. For most of other situations when disease was caused both by haplotypes with multiple rare alleles and by rare variants with similar effects, these two approaches provided similar power in testing for association.

Conclusions

The haplotype-based approach was designed to assess the role of rare and potentially causal haplotypes. The proposed rare variants-based pedigree tests were designed to assess the role of rare and potentially causal variants. This study clearly documented the situations under which either method performs better than the other. All tests have been implemented in a software, which was submitted to the Comprehensive R Archive Network (CRAN) for general use as a computer program named rvHPDT.     

Genetic variability and advance under four selection procedures in wheat pedigree breeding programme

Summary Four methods of generation advance (SPS, SSD, BP and MMS) were compared in F₃ and F₄ generations. In the F₃ generation, the SPS and SSD methods of generation advance proved superior to the BP and MMS methods for grain yield per plant and for at least one of the yield component traits. The F₃ SSD population did not differ significantly from the F₃ SPS for any of the traits. However, the F₃ SSD population retained more range and cv for different traits than with other methods of generation advance. F₄ progenies derived from F₃ SSD population were significantly superior for grain yield than lines derived from the other three F₃ populations. The MMS method of generation advance proved useful for increasing the 1,000-grain weight for which initial selection was made.Part of Ph.D. Thesis submitted by senior author to Haryana Agricultural University, Hisar     

Construction of a composite sorghum genome map and comparison with sugarcane, a related complex polyploid

 A sorghum composite linkage map was constructed with two recombinant inbred line populations using heterologous probes already mapped on maize and sugarcane. This map includes 199 loci revealed by 188 probes and distributed on 13 linkage groups. A comparison based on 84 common probes was performed between the sorghum composite map and a map of a sugarcane (Saccharum spp.) cultivar being developed and presently comprising 10 tentative linkage groups. A straight synteny was observed for 2 pairs of linkage groups; in two cases, 1 sorghum linkage group corresponded to 2 or 3 sugarcane linkage groups, respectively; in two cases 1 sugarcane link- age group corresponded to 2 separate sorghum linkage groups; for 2 sorghum linkage groups, no complete correspondance was found in the sugarcane genome. In most cases loci appeared to be colinear between homoeologous chromosomal segments in sorghum and sugarcane. These results are discussed in relation to published data on sorghum genomic maps, with specific reference to the genetic organization of sugarcane cultivars, and they, illustrate how investigations on relatively simple diploid genomes as sorghum will facilitate the mapping of related polyploid species such as sugarcane. Received: 12 August 1996 / Accepted: 30 August 1996     

Quantitative genetic dissection of complex traits in a QTL-mapping pedigree

This paper summarizes and modifies quantitative genetic analyses on a pedigree used to map genetic factors (i.e., QTLs) underlying a complex trait. The total genetic variance can be exactly estimated based on the F₂ family derived from two homozygous parents for alternative alleles at all QTLs of interest. The parents, F₁ hybrids, and two backcrosses are combined to each parent, and the total number of QTLs and the number of dominant QTLs are estimated under the assumptions of gene association with the two parents, equal gene effect, no linkage, and no epistasis among QTLs. Further relaxation for each of the assumptions are made in detail. The biometric estimator for the QTL number and action mode averaged over the entire genome could provide some basic and complementary information to QTL mapping designed to detect the effect and location of specific genetic factors.     

Genetics of nonsenescence and charcoal rot resistance in sorghum

Summary Nonsenescence is a delayed leaf and plant death resistance mechanism in sorghum that circumvents the detrimental effects of reduced soil moisture combined with high temperatures during post-anthesis growth. This drought-tolerance mechanism is often equated with charcoal rot resistance, a widespread root and stalk disease of great destructive potential. Therefore, the inheritance of charcoal rot resistance was investigated directly, by exposure of sorghum to Macrophomina phaseolina, the causal organism, and indirectly, by determination of the inheritance of nonsenescence. Sorghum families derived from diallel crosses between two nonsenescent, resistant inbreds (B35, SC599-11E) and two senescent, susceptible inbreds (BTx378, BTx623) were evaluated in 1989 at College Station and at Lubbock, Texas, under controlled and field conditions. We determined that nonsenescence was regulated by dominant and recessive epistatic interactions between two nonsenescence-inducing loci and a third locus with modifying effects. The same conclusion was reached for charcoal rot resistance. The presence of different genetic mechanisms within SC599-11E for nonsenescence and charcoal rot resistance verifies that these two forms of resistance are not different manifestations of a single trait, i.e., they are not to be equated with each other. We conclude that nonsenescence alone cannot account for, and should not be used as the sole breeding criterion for, resistance to charcoal rot in sorghum.     

Marker-based estimates of identity by descent and alikeness in state among maize inbreds

Molecular markers are useful for determining relationships and similarity among inbreds, especially if the proportion of marker loci with alleles common to inbreds i and j is partitioned into: (1) the probability that marker alleles are identical by descent (_Mf_ij); and (2) the conditional probability that marker alleles are alike in state, given that they are not identical by descent ( _ij). Our objectives were to: develop a method, based on tabular analysis of restriction fragment length polymorphism marker data, for estimating _Mf_ij, _ij, and the parental contribution to inbred progeny; validate the accuracy of the method with a simulated data set; and compare the pedigree-based coefficient of coancestry (f_ij) and _Mf_ij among a set of maize (Zea mays L.) inbreds. Banding patterns for 73 probeenzyme combinations were determined among 13 inbreds. Iterative estimation of _Mf_ij, _ij, and the parental contribution to progeny was performed with procedures similar to a tabular analysis of pedigree data. Deviations of _Mf_ij from pedigree-based f_ij ranged from 0.002 to 0.288, indicating large effects of selection and/or drift during inbreeding for some inbreds. Differences between marker-based estimates and expected values of parental contribution to inbred progeny were as large as 0.205. Results for a simulated set of inbreds indicated that tabular analysis of marker data provides more accurate estimates of _Mf_ij and _ij than other methods described in the literature. Tabular analysis requires the availability of marker data for all the progenitors of each inbred. When marker data are not available for the parents of a given inbred, _Mf_ij and _ij may still be calculated if parental contributions to the inbred are assumed equal to their expectations.     

应用二种定位法比较不同世代水稻产量性状QTL的检测结果

应用珍汕97B／密阳46的F2和重组自交系（RIL）群体,建立RFLP连锁图,检测控制稻谷产量及其5个构成因子的QTL。结果表明,具有较大加性效应者,能同时在F2和RIL群体中检测到。而且,在重组自交系群体中,发现设重复的表型鉴定与基于单株的表型鉴定,对效应较高的QTL的检测影响不大。     

Identification of genomic regions associated with stay green in sorghum by testing RILs in multiple environments

Stay green is an important drought resistance trait for sorghum production. QTLs for this trait with consistent effects across a set of environments would increase the efficiency of selection because of its relatively low heritability. One hundred and sixty recombinant inbreds, derived from a cross between QL39 and QL41, were used as a segregating population for genome mapping and stay green evaluation. Phenotypic data were collected in replicated field trials from five sites and in three growing seasons, and analysed by fitting appropriate models to account for spatial variability and to describe the genotype by environment interaction. Interval mapping and non-parametric mapping identified three regions, each in a separate linkage group, associated with stay green in more than one trial, and two regions in single trial. The regions on linkage groups B and I were both consistently identified from three trials. The multiple environment testing was very helpful for correctly identifying QTLs associated with the trait. The utilisation of molecular markers for stay green in sorghum breeding is also discussed. Received: 22 March 1999 / Accepted: 11 November 1999     

Estimation of pairwise identity by descent from dense genetic marker data in a population sample of haplotypes

I present a new approach for calculating probabilities of identity by descent for pairs of haplotypes. The approach is based on a joint hidden Markov model for haplotype frequencies and identity by descent (IBD). This model allows for linkage disequilibrium, and the method can be applied to very dense marker data. The method has high power for detecting IBD tracts of genetic length of 1 cM, with the use of sufficiently dense markers. This enables detection of pairwise IBD between haplotypes from individuals whose most recent common ancestor lived up to 50 generations ago.     

Mapping of post-flowering drought resistance traits in grain sorghum: association between QTLs influencing premature senescence and maturity

The identification of genetic factors underlying the complex responses of plants to drought stress provides a solid basis for improving drought resistance. The stay-green character in sorghum (Sorghum bicolor L. Moench) is a post-flowering drought resistance trait, which makes plants resistant to premature senescence under drought stress during the grainfilling stage. The objective of this study was to identify quantitative trait loci (QTLs) that control premature senescence and maturity traits, and to investigate their association under post-flowering drought stress in grain sorghum. A genetic linkage map was developed using a set of recombinant inbred lines (RILs) obtained from the cross B35 × Tx430, which were scored for 142 restriction fragment length polymorphism (RFLP) markers. The RILs and their parental lines were evaluated for post-flowering drought resistance and maturity in four environments. Simple interval mapping identified seven stay-green QTLs and two maturity QTLs. Three major stay-green QTLs (SGA, SGD and SGG) contributed to 42% of the phenotypic variability (LOD 9.0) and four minor QTLs (SGB, SGI.1, SGI.2, and SGJ) significantly contributed to an additional 25% of the phenotypic variability in stay-green ratings. One maturity QTL (DFB) alone contributed to 40% of the phenotypic variability (LOD 10.0), while the second QTL (DFG) significantly contributed to an additional 17% of the phenotypic variability (LOD 4.9). Composite interval mapping confirmed the above results with an additional analysis of the QTL × Environment interaction. With heritability estimates of 0.72 for stay-green and 0.90 for maturity, the identified QTLs explained about 90% and 63% of genetic variability for stay-green and maturity traits, respectively. Although stay-green ratings were significantly correlated (r=0.22, P ≤ 0.05) with maturity, six of the seven stay-green QTLs were independent of the QTLs influencing maturity. Similarly, one maturity QTL (DFB) was independent of the stay-green QTLs. One stay-green QTL (SGG), however, mapped in the vicinity of a maturity QTL (DFG), and all markers in the vicinity of the independent maturity QTL (DFB) were significantly (P ≤ 0.1) correlated with stay-green ratings, confounding the phenotyping of stay-green. The molecular genetic analysis of the QTLs influencing stay-green and maturity, together with the association between these two inversely related traits, provides a basis for further study of the underlying physiological mechanisms and demonstrates the possibility of improving drought resistance in plants by pyramiding the favorable QTLs. Received: 10 October 1998 / Accepted: 12 July 1999     

Identification of genomic regions that affect grain-mould incidence and other traits of agronomic importance in sorghum

Grain-mould is a major problem in grain sorghum utilization as mouldy grain has a reduced quality due to the deterioration of the endosperm and reduced embryo viability. Here, our objective was to use genome mapping to improve knowledge of genetic variation and co-variation for grain-mould incidence and other inter-related agronomic traits. Grain-mould incidence, kernel-milling hardness, grain density, plant height, panicle peduncle length, foliar-disease incidence, and plant color were measured on 125 F₅ genotypes derived from a cross of Sureño and RTx430. Quantitative trait loci were detected by means of 130 mapped markers (44 microsatellites, 85 AFLPs, one morphological-trait locus) distributed among ten linkage groups covering 970 cM. One to five QTLs affected each trait, with the exception of grain density for which no QTLs were detected. Grain-mould incidence was affected by five QTLs each accounting for between 10 and 23% of the phenotypic variance. The effects and relative positions of QTLs for grain-mould incidence were in accordance with the QTL distribution of several inter-related agronomic traits (e.g., plant height, peduncle length) and with the correlation between these phenotypic traits and grain-mould incidence. The detection of QTLs for grain-mould incidence was dependent on the environment, which is consistent with heritibility estimates that show strong environmental and genotype × environment effects. Several genomic regions affected multiple traits including one region that affected grain-mould incidence, plant height, panicle peduncle length, and grain-milling hardness, and a second region that influenced grain-mould (in four environments) and plant height. One genomic region, which harbors loci for plant color, influenced the severity of foliar disease symptoms and the incidence of grain-mould in one environment. Collectively QTLs detected in the present population explained between 10% and 55% of the phenotypic variance observed for a given trait.     

An approximate likelihood for genetic data under a model with recombination and population splitting

We describe a new approximate likelihood for population genetic data under a model in which a single ancestral population has split into two daughter populations. The approximate likelihood is based on the ‘Product of Approximate Conditionals’ likelihood and ‘copying model’ of Li and Stephens [Li, N., Stephens, M., 2003. Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data. Genetics 165 (4), 2213–2233]. The approach developed here may be used for efficient approximate likelihood-based analyses of unlinked data. However our copying model also considers the effects of recombination. Hence, a more important application is to loosely-linked haplotype data, for which efficient statistical models explicitly featuring non-equilibrium population structure have so far been unavailable. Thus, in addition to the information in allele frequency differences about the timing of the population split, the method can also extract information from the lengths of haplotypes shared between the populations. There are a number of challenges posed by extracting such information, which makes parameter estimation difficult. We discuss how the approach could be extended to identify haplotypes introduced by migrants.     

Comparison of a set of allelic QTL-NILs for chromosome 4 of tomato: Deductions about natural variation and implications for germplasm utilization

Quantitative Trait Locus (QTL) allelic variation was studied by analyzing near-isogenic lines (NILs) carrying homologous introgressions on chromosome 4 from three green-fruited wild tomato species. The NILs affect agronomic (yield, brix, fruit weight) and fruit (fruit shape, color, epidermal reticulation) traits in a similar manner. However, significant differences were detected in the magnitudes of the effects, the dominance deviations and epistatic interactions, indicating that those species carry different alleles for the QTL. As the QTL did not show any interaction across environments, gene-tic backgrounds or other QTLs, it can be used to introduce novel genetic variation into a broad range of cultivars. Analysis of new recombinant NILs showed that fruit traits are controlled by several linked genetic loci, whereas multiple genetic loci control the agronomic traits within the original introgression. The hypothesis that QTLs may be composed of multiple linked genes can not be rejected prior to implement projects for QTL isolation and cloning. Loci involved in color enhancement could not be related to any known gene involved in the carotenoid biosynthesis pathway, therefore it is hypothesized that the function of those loci must be related to the genetic regulation of the carotenoid biosynthetic pathway. Received: 14 April 2000 / Accepted: 12 May 2000     

Similarity by state/descent and genetic vector spaces: analysis of a longitudinal family study

Using the genome-wide screening data of the Framingham Heart Study (394 nuclear families, 1328 genotyped subjects, 397 marker loci) we have quantified the underlying genetic diversity through high-dimensional genetic feature vectors and constructed a genetic vector space for the analysis of population substructure. Adaptive clustering procedures led to three major subgroups that were regarded as being related to "biological" ethnicity and that included more than 70% of the subjects. Based on these subgroups we addressed the question of ethnicity-related and ethnicity-independent risk factors for coronary heart disease (CHD). To this end, we relied upon hypertension as an endophenotype of CHD and applied a multivariate sib-pair method in order to search for oligogenic marker configurations for which the sib-sib similarities deviated from the parent-offspring similarities. Indeed, the latter similarities are always "0.5" irrespective of the affection status of parents and offspring. Loci with significant contributions to the oligogenic marker configuration constituted a CHD-specific genetic vector space. We found several ethnicity-independent signals. One signal on chromosome 8 may relate to the CYP11B1/CYP11B2 genes.