Hexaploid bread wheat (Triticum aestivum L. em. Thell) is one of the world's most important crop plants and displays a very low level of intraspecific polymorphism. We report the development of highly polymorphic microsatellite markers using procedures optimized for the large wheat genome. The isolation of microsatellite-containing clones from hypomethylated regions of the wheat genome increased the proportion of useful markers almost twofold. The majority (80%) of primer sets developed are genome-specific and detect only a single locus in one of the three genomes of bread wheat (A, B, or D). Only 20% of the markers detect more than one locus. A total of 279 loci amplified by 230 primer sets were placed onto a genetic framework map composed of RFLPs previously mapped in the reference population of the International Triticeae Mapping Initiative (ITMI) Opata 85 x W7984. Sixty-five microsatellites were mapped at a LOD >2.5, and 214 microsatellites were assigned to the most likely intervals. Ninety-three loci were mapped to the A genome, 115 to the B genome, and 71 to the D genome. The markers are randomly distributed along the linkage map, with clustering in several centromeric regions.

https://www.genetics.org/content/genetics/149/4/2007.full.pdf

A microsatellite map of wheat.

Nearly a century has been spent collecting and preserving genetic diversity in plants. Germplasm banks-living seed collections that serve as repositories of genetic variation-have been established as a source of genes for improving agricultural crops. Genetic linkage maps have made it possible to study the chromosomal locations of genes for improving yield and other complex traits important to agriculture. The tools of genome research may finally unleash the genetic potential of our wild and cultivated germplasm resources for the benefit of society.

http://www3.botany.ubc.ca/rieseberglab/plantevol/Tanksley%201997%20Seed%20banks%20and%20molecular%20maps.pdf

Seed Banks and Molecular Maps: Unlocking Genetic Potential from the Wild

A microsatellite consensus map was constructed by joining four independent genetic maps of bread wheat. Three of the maps were F1-derived, doubled-haploid line populations and the fourth population was ‘Synthetic’ × ‘Opata’, an F6-derived, recombinant-inbred line population. Microsatellite markers from different research groups including the Wheat Microsatellite Consortium, GWM, GDM, CFA, CFD, and BARC were used in the mapping. A sufficient number of common loci between genetic maps, ranging from 52 to 232 loci, were mapped on different populations to facilitate joining the maps. Four genetic maps were developed using MapMaker V3.0 and JoinMap V3.0. The software CMap, a comparative map viewer, was used to align the four maps and identify potential errors based on consensus. JoinMap V3.0 was used to calculate marker order and recombination distances based on the consensus of the four maps. A total of 1,235 microsatellite loci were mapped, covering 2,569 cM, giving an average interval distance of 2.2 cM. This consensus map represents the highest-density public microsatellite map of wheat and is accompanied by an allele database showing the parent allele sizes for every marker mapped. This enables users to predict allele sizes in new breeding populations and develop molecular breeding and genomics strategies.

A high-density microsatellite consensus map for bread wheat (Triticum aestivum L.)

Oilseed rape (Brassica napus L.) was formed ~7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72× genome multiplication since the origin of angiosperms and high gene content. We examined the B. napus genome and the consequences of its recent duplication. The constituent An and Cn subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement.

http://science.sciencemag.org/content/sci/345/6199/950.full.pdf

Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome

DNA markers have enormous potential to improve the efficiency and precision of conventional plant breeding via marker-assisted selection (MAS). The large number of quantitative trait loci (QTLs) mapping studies for diverse crops species have provided an abundance of DNA marker–trait associations. In this review, we present an overview of the advantages of MAS and its most widely used applications in plant breeding, providing examples from cereal crops. We also consider reasons why MAS has had only a small impact on plant breeding so far and suggest ways in which the potential of MAS can be realized. Finally, we discuss reasons why the greater adoption of MAS in the future is inevitable, although the extent of its use will depend on available resources, especially for orphan crops, and may be delayed in less-developed countries. Achieving a substantial impact on crop improvement by MAS represents the great challenge for agricultural scientists in the next few decades.

/pdf/marker-assisted-selection-an-approach-for-precision-plant-1be57ryhno.pdf

Marker-assisted selection: an approach for precision plant breeding in the twenty-first century

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.

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

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.

QGENE: software for marker-based genomic analysis and breeding

A molecular-marker linkage map of hexaploid wheat (Triticum aestivum L. em. Thell) provides a framework for integration with teh classical genetic map and a record of the chromosomal rearrangements involved in the evolution of this crop species. We have constructed restriction fragment length polymorphism (RFLP) maps of the A-, B-, and D-genome chromosomes of homoeologous groups 4, 5, and 7 of wheat using 114 F7 lines from a synthetic X cultivated wheat cross and clones from 10 DNA libraries. Chromosomal breakpoints for known ancestral reciprocal translocations involving these chromosomes and for a known pericentric inversion on chromosome 4A were localized by linkage and aneuploid analysis. Known genes mapped include the major vernalization genes Vrn1 and Vrn3 on chromosome arms 5AL and 5DL, the red-coleoptile gene Rc1 on 7AS, and presumptively the leaf-rust (Puccinia recondita f.sp. tritici) resistance gene Lr34 on 7DS and the kernel-hardness gene Ha on 5DS. RFLP markers previously obtained for powdery-mildew (Blumeria graminis f.sp. tritici) resistance genes Pm2 and Pm1 were localized on chromosome arms 5DS and 7AL.

https://www.genetics.org/content/genetics/141/2/721.full.pdf

Molecular mapping of wheat: major genes and rearrangements in homoeologous groups 4, 5, and 7.

Summary: 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.

Contact: jcn@ksu.edu

QGene 4.0, an extensible Java QTL-analysis platform

Group 1 chromosomes of the Triticeae tribe have been studied extensively because many important genes have been assigned to them In this paper, chromosome 1 linkage maps of Triticum aestivum, T tauschii, and T monococcum are compared with existing barley and rye maps to develop a consensus map for Triticeae species and thus facilitate the mapping of agronomic genes in this tribe The consensus map that was developed consists of 14 agronomically important genes, 17 DNA markers that were derived from known-function clones, and 76 DNA markers derived from anonymous clones There are 12 inconsistencies in the order of markers among seven wheat, four barley, and two rye maps A comparison of the Triticeae group 1 chromosome consensus map with linkage maps of homoeologous chromosomes in rice indicates that the linkage maps for the long arm and the proximal portion of the short arm of group 1 chromosomes are conserved among these species Similarly, gene order is conserved between Triticeae chromosome 1 and its homoeologous chromosome in oat The location of the centromere in rice and oat chromosomes is estimated from its position in homoeologous group 1 chromosomes of Triticeae

/pdf/molecular-genetic-maps-for-group-1-chromosomes-of-triticeae-4z3gvodqhx.pdf

James C. Nelson

Papers

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

QGENE: software for marker-based genomic analysis and breeding

Molecular mapping of wheat: major genes and rearrangements in homoeologous groups 4, 5, and 7.

QGene 4.0, an extensible Java QTL-analysis platform

Molecular-genetic maps for group 1 chromosomes of triticeae species and their relation to chromosomes in rice and oat