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     

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.     

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     

Large‐scale GWAS in sorghum reveals common genetic control of grain size among cereals

Grain size is a key yield component of cereal crops and a major quality attribute. It is determined by a genotype’s genetic potential and its capacity to fill the grains. This study aims to dissect the genetic architecture of grain size in sorghum. An integrated genome‐wide association study (GWAS) was conducted using a diversity panel (n = 837) and a BC‐NAM population (n = 1421). To isolate genetic effects associated with genetic potential of grain size, rather than the genotype’s capacity to fill the grains, a treatment of removing half of the panicle was imposed during flowering. Extensive and highly heritable variation in grain size was observed in both populations in 5 field trials, and 81 grain size QTL were identified in subsequent GWAS. These QTL were enriched for orthologues of known grain size genes in rice and maize, and had significant overlap with SNPs associated with grain size in rice and maize, supporting common genetic control of this trait among cereals. Grain size genes with opposite effect on grain number were less likely to overlap with the grain size QTL from this study, indicating the treatment facilitated identification of genetic regions related to the genetic potential of grain size. These results enhance understanding of the genetic architecture of grain size in cereal, and pave the way for exploration of underlying molecular mechanisms and manipulation of this trait in breeding practices.     

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     

Mapping and breeding value evaluation of a semi-dominant semidwarf gene in upland rice

Plant height is an important trait related to yield potential and plant architecture. A suitable plant height plays a crucial role in improvement of rice yield and lodging resistance. In this study, we found that the traditional upland landrace ‘Kaowenghan’ (KWH) showed a special semi-dwarf phenotype. To identify the semi-dwarf gene from KWH, we raised BC₂F₄ semi-dwarf introgression lines (IL) by hybridization of the japonica rice cultivar ‘Dianjingyou1’ (DJY1) and KWH in a DJY1 background. The plant height of the homozygous semi-dwarf IL (IL-87) was significantly reduced compared with that of DJY1. The phenotype of the F₁ progeny of the semi-dwarf IL-87 and DJY1 showed that the semi-dwarf phenotype was semidominant. QTL mapping indicated that the semi-dwarf phenotype was controlled by a major QTL qDH1 and was localized between the markers RM6696 and RM12047 on chromosome 1. We also developed near-isogenic lines (NIL) from the BC₃F₃ population, and found that the yield of homozygous NIL (NIL-2) was not significantly different compared to DJY1. Breeding value evaluation through investigation of the plant height of the progeny of NIL (NIL-2) and cultivars from different genetic background indicate that the novel semi-dwarf gene shows potential as a genetic resource for rice breeding.     

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.     

高油酸花生遗传育种研究进展

花生是我国重要的油料作物,子仁中油酸和亚油酸的含量达到80%左右,其中油酸是影响花生油理化稳定性和营养价值的重要品质指标。十五以来,为进一步提升我国花生国际竞争力和满足国内人们对高品质花生油的消费需求,培育高油酸花生品种成为我国重要的花生品质育种目标之一。本文综述了国内外高油酸花生突变体、高油酸含量性状的遗传规律和分子机理、育成发放的高油酸花生品种的研究进展,对高油酸花生品种系谱、育成方式进行分析。分析高油酸花生育种中存在的问题,以期为我国高油酸花生育种提供参考。     

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     

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.     

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     

Converting multi-trait breeding objectives into operative selection indexes to ensure genetic gains in low-input sheep and goat breeding programmes

Small ruminant breeding programmes in low-input production systems are best organised at the community level. Participant farmers have to agree on goal traits and their relative importance. When BLUP breeding values of goal traits are not available in time, appropriate selection indexes can be used to aid visual selection. Taking Ethiopian Abergelle goat and Bonga sheep community-based breeding programmes (CBBPs) as an example, breeding objective functions were defined and selection indexes were constructed and evaluated. Breeding goals for Abergelle goats included early sale weight, survival and milk production. Breeding goals for Bonga included the number of offspring born, sale weight and survival. Economic weights of objective traits can be used in several ways depending on measured traits and the reliability of their genetic parameters. Selection indexes included combinations of objective traits measured on candidates and their dams and situations when Abergelle communities prefer to restrict genetic changes in number of offspring born or adult weight and when Bonga communities prefer to restrict changes in adult weight. Genetic and economic gains were evaluated as well as sensitivity to feed cost assumptions and to repeated dam records. After independent culling on preponderant traits such as coat colour and horn/tail type, sires in Abergelle goat community breeding programmes should be selected on indexes including at least own early live weight and their dams average milk production records. Sires for Bonga sheep programmes should be selected on own early live weight and desirably also on their dam’s number of offspring born. Sensitivity to feed cost assumptions was negligible but repeated measurements of dam records improved index accuracies considerably. Restricting genetic changes in number of offspring born or adult weight is not recommended.     

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.     

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.     

Domestication and the storage starch biosynthesis pathway: signatures of selection from a whole sorghum genome sequencing strategy

Next‐generation sequencing of complete genomes has given researchers unprecedented levels of information to study the multifaceted evolutionary changes that have shaped elite plant germplasm. In conjunction with population genetic analytical techniques and detailed online databases, we can more accurately capture the effects of domestication on entire biological pathways of agronomic importance. In this study, we explore the genetic diversity and signatures of selection in all predicted gene models of the storage starch synthesis pathway of Sorghum bicolor, utilizing a diversity panel containing lines categorized as either ‘Landraces’ or ‘Wild and Weedy’ genotypes. Amongst a total of 114 genes involved in starch synthesis, 71 had at least a single signal of purifying selection and 62 a signal of balancing selection and others a mix of both. This included key genes such as STARCH PHOSPHORYLASE 2 (SbPHO2, under balancing selection), PULLULANASE (SbPUL, under balancing selection) and ADP‐glucose pyrophosphorylases (SHRUNKEN2, SbSH2 under purifying selection). Effectively, many genes within the primary starch synthesis pathway had a clear reduction in nucleotide diversity between the Landraces and wild and weedy lines indicating that the ancestral effects of domestication are still clearly identifiable. There was evidence of the positional rate variation within the well‐characterized primary starch synthesis pathway of sorghum, particularly in the Landraces, whereby low evolutionary rates upstream and high rates downstream in the metabolic pathway were expected. This observation did not extend to the wild and weedy lines or the minor starch synthesis pathways.     

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。     

Largely unlinked gene sets targeted by selection for domestication syndrome phenotypes in maize and sorghum

The domestication of diverse grain crops from wild grasses was a result of artificial selection for a suite of overlapping traits producing changes referred to in aggregate as ‘domestication syndrome’. Parallel phenotypic change can be accomplished by either selection on orthologous genes or selection on non‐orthologous genes with parallel phenotypic effects. To determine how often artificial selection for domestication traits in the grasses targeted orthologous genes, we employed resequencing data from wild and domesticated accessions of Zea (maize) and Sorghum (sorghum). Many ‘classic’ domestication genes identified through quantitative trait locus mapping in populations resulting from wild/domesticated crosses indeed show signatures of parallel selection in both maize and sorghum. However, the overall number of genes showing signatures of parallel selection in both species is not significantly different from that expected by chance. This suggests that while a small number of genes will extremely large phenotypic effects have been targeted repeatedly by artificial selection during domestication, the optimization part of domestication targeted small and largely non‐overlapping subsets of all possible genes which could produce equivalent phenotypic alterations.