James C. Nelson

Advanced backcross QTL analysis: a method for the simultaneous discovery and transfer of valuable QTLs from unadapted germplasm into elite breeding lines

Advanced backcross QTL analysis is proposed as a method of combining QTL analysis with variety development. It is tailored for the discovery and transfer of valuable QTL alleles from unadapted donor lines (e.g., land races, wild species) into established elite inbred lines. Following this strategy, QTL analysis is delayed until the BC2 or BC3 generation and, during the development of these populations, negative selection is exercised to reduce the frequency of deleterious donor alleles. Simulations suggest that advanced backcross QTL analysis will be effective in detecting additive, dominant, partially dominant, or overdominant QTLs. Epistatic QTLs or QTLs with gene actions ranging from recessive to additive will be detected with less power than in selfing generations. QTL-NILs can be derived from advanced backcross populations in one or two additional generations and utilized to verify QTL activity. These same QTL-NILs also represent commercial inbreds improved (over the original recurrent inbred line) for one or more quantitative traits. The time lapse from QTL discovery to construction and testing of improved QTL-NILs is minimal (1–2 years). If successfully employed, advanced backcross QTL analysis can open the door to exploiting unadapted and exotic germplasm for the quantitative trait improvement of a number of crop plants.

QGENE: software for marker-based genomic analysis and breeding

Efficient use of DNA markers for genomic research and crop improvement will depend as much on computational tools as on laboratory technology. The large size and multidimensional character of marker datasets invite novel approaches to data visualization. Described here is a software application embodying two design principles: conventional reduction of raw genetic marker data to numerical summary statistics, and fast, interactive graphical display of both data and statistics. The program performs various analyses for mapping quantitative-trait loci in real or simulated datasets and other analyses in aid of phenotypic and marker-assisted breeding. Functionality is described and some output is illustrated.

Comparative mapping in grasses. Oat relationships

The development of RFLP linkage maps in hexaploid and diploid oat allows us to study genetic relationships of these species at the DNA level. In this report, we present the extension of a previously developed diploid oat map (Avena atlantica x A. hirtula) and its molecular-genetic relationships with wheat, rice and maize. Examination of 92–99% of the length of the oat genome map with probes common to Triticeae species, rice or maize showed that 84, 79 and 71%, respectively, was conserved between these species and oat. Generally, the orders of loci among chromosomes homoeologous to oat chromosomes A and D were the most conserved and those of chromosomes homoeologous to oat chromosome G were the least conserved. Conservation was observed for blocks ranging from whole chromosomes 101 cM long to small segments 2.5 cM long containing two loci. Comparison of the homoeologous segments of Triticeae, rice and maize relative to oat indicated that certain regions have been maintained in all four species. The relative positions of major genes governing traits such as seed storage proteins and resistance to leaf rusts have been conserved between cultivated oat and Triticeae species. Also, the locations of three vernalization/or photo-period response genes identified in hexaploid oat correspond to the locations of similar genes in homoeologous chromosomes of wheat, rice or maize. The locations of the centromeres for six of the seven oat chromosomes were estimated based on the homoeologous segments between oat and Triticeae chromosomes.

Linkage between RFLP markers and genes affecting kernel hardness in wheat

A molecular-marker linkage map of wheat (Triticum aestivum L. em. Thell) provides a powerful tool for identifying genomic regions influencing breadmaking quality. A variance analysis for kernel hardness was conducted using 114 recombinant inbred lines (F7) from a cross between a synthetic and a cultivated wheat. The major gene involved in kernel hardness, ha (hard), known to be on chromosome arm 5DS, was found to be closely linked with the locus Xmta9 corresponding to the gene of puroindoline-a. This locus explained around 63% of the phenotypic variability but there was no evidence that puroindoline-a is the product of Ha (soft). Four additional regions located on chromosomes 2A, 2D, 5B, and 6D were shown to have single-factor effects on hardness, while three others situated on chromosomes 5A, 6D and 7A had interaction effects. Positive alleles were contributed by both parents. A three-marker model explains about 75% of the variation for this trait.

QGene 4.0, an extensible Java QTL-analysis platform

UNLABELLED Of many statistical methods developed to date for quantitative trait locus (QTL) analysis, only a limited subset are available in public software allowing their exploration, comparison and practical application by researchers. We have developed QGene 4.0, a plug-in platform that allows execution and comparison of a variety of modern QTL-mapping methods and supports third-party addition of new ones. The software accommodates line-cross mating designs consisting of any arbitrary sequence of selfing, backcrossing, intercrossing and haploid-doubling steps that includes map, population, and trait simulators; and is scriptable. AVAILABILITY Software and documentation are available at http://coding.plantpath.ksu.edu/qgene. Source code is available on request.

Advanced backcross QTL analysis of a hard winter wheat × synthetic wheat population

Advanced backcross quantitative trait locus (AB-QTL) analysis was used to identify QTLs for yield and yield components in a backcross population developed from a cross between hard red winter wheat (Triticum aestivum L.) variety Karl 92 and the synthetic wheat line TA 4152-4. Phenotypic data were collected for agronomic traits including heading date, plant height, kernels per spike, kernel weight, tiller number, biomass, harvest index, test weight, grain yield, protein content, and kernel hardness on 190 BC2F2:4 lines grown in three replications in two Kansas environments. Severity of wheat soilborne mosaic virus (WSBMV) reaction was evaluated at one location. The population was genotyped using 151 microsatellite markers. Of the ten putative QTLs identified, seven were located on homoeologous group 2 and group 3 chromosomes. The favorable allele was contributed by cultivated parent Karl 92 at seven QTLs including a major one for WSBMV resistance, and by the synthetic parent at three QTLs: for grain hardness, kernels per spike, and tiller number.

Quantitative trait locus analysis of wheat quality traits

Milling and baking quality traits in wheat (Triticum aestivum L.) were studied by QTL analysis in the ITMI population, a set of 114 recombinant inbred lines (RILs) generated from a synthetic-hexaploid (W7985) × bread-wheat (Opata 85) cross. Grain from RILs grown in U.S., French, and Mexican wheat-growing regions was assayed for kernel-texture traits, protein concentration and quality, and dough strength and mixing traits. Only kernel-texture traits showed similar genetic control in all environments, with Opata ha alleles at the hardness locus Ha on chromosome arm 5DS increasing grain hardness, alkaline water retention capacity, and flour yield. Dough strength was most strongly influenced by Opata alleles at 5DS loci near or identical to Ha. Grain protein concentration was associated not with high-molecular-weight glutenin loci but most consistently with the Gli-D2 gliadin locus on chromosome arm 6DS. In Mexican-grown material, a 2DS locus near photoperiod-sensitivity gene Ppd1 accounted for 25% of variation in protein, with the ppd1-coupled allele associated with higher (1.1%) protein concentration. Mixogram traits showed most influence from chromosomal regions containing gliadin or low-molecular-weight glutenin loci on chromosome arms 1AS, 1BS, and 6DS, with the synthetic hexaploid contributing favorable alleles.Some RI lines showed quality values consistently superior to those of the parental material, suggesting the potential of further evaluating new combinations of alleles from diploid and tetraploid relatives, especially alleles of known storage proteins, for improvement of quality traits in wheat cultivars.

Introgression and DNA marker analysis of Lycopersicon peruvianum, a wild relative of the cultivated tomato, into Lycopersicon esculentum, followed through three successive backcross generations

Abstract Segregation of the Lycopersicon peruvianum genome was followed through three generations of backcrossing to the cultivated tomato L. esculentum cv ‘E6203’ using molecular markers. Thirteen BC1 plants were genotyped with 113 markers, 67 BC2 plants with 84 markers, and finally 241 BC3 plants were genotyped with 177 markers covering the entire genome and a BC3 map constructed. Several segments of the genome, including parts of chromosomes 3, 4, 6, and 10, quickly became fixed for esculentum alleles, possibly due to sterility problems encountered in the BC1. Observed overall heterozygosity and chromosome segment lengths at each generation were very near the expected theoretical values. Markers located near the top telomeric region of chromosome 9 showed segregation highly skewed towards the wild allele through all generations, suggesting the presence of a gamete promoter gene. One markers, TG9, mapped to a new position on chromosome 9, implying an intrachromosomal translocation event. Despite the great genetic distance between the two parents, overall recombination was only 25% less than that observed in a previous tomato cross, indicating that L. peruvianum genes may be more readily introgressed into cultivated germplasm than originally believed.

Single-nucleotide polymorphism discovery by high-throughput sequencing in sorghum

BackgroundEight diverse sorghum (Sorghum bicolor L. Moench) accessions were subjected to short-read genome sequencing to characterize the distribution of single-nucleotide polymorphisms (SNPs). Two strategies were used for DNA library preparation. Missing SNP genotype data were imputed by local haplotype comparison. The effect of library type and genomic diversity on SNP discovery and imputation are evaluated.ResultsAlignment of eight genome equivalents (6 Gb) to the public reference genome revealed 283,000 SNPs at ≥82% confirmation probability. Sequencing from libraries constructed to limit sequencing to start at defined restriction sites led to genotyping 10-fold more SNPs in all 8 accessions, and correctly imputing 11% more missing data, than from semirandom libraries. The SNP yield advantage of the reduced-representation method was less than expected, since up to one fifth of reads started at noncanonical restriction sites and up to one third of restriction sites predicted in silico to yield unique alignments were not sampled at near-saturation. For imputation accuracy, the availability of a genomically similar accession in the germplasm panel was more important than panel size or sequencing coverage.ConclusionsA sequence quantity of 3 million 50-base reads per accession using a Bsr FI library would conservatively provide satisfactory genotyping of 96,000 sorghum SNPs. For most reliable SNP-genotype imputation in shallowly sequenced genomes, germplasm panels should consist of pairs or groups of genomically similar entries. These results may help in designing strategies for economical genotyping-by-sequencing of large numbers of plant accessions.

Chromosomal locations and genetic relationships of tiller and spike characters in wheat

Number of tillers per plant, plant growth habit in seedling and adult stages, and spike and spikelet characters are agronomically important features of the gross morphology of wheat. To localize to wheat chromosomes the genes for these traits, we scored them in a set of wheat recombinant-inbred mapping lines already well genotyped with molecular markers. Quantitative-trait analysis revealed a region near Gli-A2 (Xpsr10) on the short arm of chromosome 6A strongly affecting tiller number and the correlated trait of seedling growth habit. Genes with opposing effects on adult plant type were localized on the short arms of chromosomes2A and 3A, while genes affecting spike development were assigned to several A- and B-genome chromosomes. None of these genes showed synteny with counterpart QTLs reported to affect the same traits in rice. In the chromosome 2D region containing the photoperiod-insensitivity gene Ppd-D1, the major determinant of heading date in these autumn-sown lines, earliness alleles reduced tiller and spikelet numbers and increased erect seedling growth habit, but showed no influence on adult plant type or spike length. Though several of these morphological traits are generally considered to be associated with winter hardiness and their phenotypic intercorrelations were consistent with the genetic mapping evidence, no association was found between newly identified loci and known vernalization-response or frost-resistance loci.