Comparative mapping

Chickpea is a cool season grain legume of exceptionally high nutritive value and most versatile food use. It is mostly grown under rain fed conditions in arid and semi-arid areas around the world. Despite growing demand and high yield potential, chickpea yield is unstable and productivity is stagnant at unacceptably low levels. Major yield increases could be achieved by development and use of cultivars that resist/tolerate abiotic and biotic stresses. In recent years the wide use of early maturing cultivars that escape drought stress led to significant increases in chickpea productivity. In the Mediterranean region, yield could be increased by shifting the sowing date from spring to winter. However, this is hampered by the sensitivity of the crop to low temperatures and the fungal pathogen Ascochyta rabiei. Drought, pod borer (Helicoverpa spp.) and the fungus Fusarium oxysporum additionally reduce harvests there and in other parts of the world. Tolerance to rising salinity will be a future advantage in many regions. Therefore, chickpea breeding focuses on increasing yield by pyramiding genes for resistance/tolerance to the fungi, to pod borer, salinity, cold and drought into elite germplasm. Progress in breeding necessitates a better understanding of the genetics underlying these traits. Marker-assisted selection (MAS) would allow a better targeting of the desired genes. Genetic mapping in chickpea, for a long time hampered by the little variability in chickpea’s genome, is today facilitated by highly polymorphic, co-dominant microsatellite-based markers. Their application for the genetic mapping of traits led to inter-laboratory comparable maps. This paper reviews the current situation of chickpea genome mapping, tagging of genes for ascochyta blight, fusarium wilt resistance and other traits, and requirements for MAS. Conventional breeding strategies to tolerate/avoid drought and chilling effects at flowering time, essential for changing from spring to winter sowing, are described. Recent approaches and future prospects for functional genomics of chickpea are discussed.

Hazardous industrial sites have always represented a threat for the community often provoking major accidents overcoming the boundaries of the plants and affecting the surrounding urban areas. If the industrial sites are located in natural hazard-prone areas, technological accidents may be triggered by natural events, generating so-called na-tech events which may modify and increase the impact and the overall damage in the areas around them. Nevertheless, natural and technological hazards are still treated as two separate issues, and up to now the methods for na-tech risk assessment have been developed mainly for specific natural hazards, generally restricted to some plant typologies and to the area of the plant itself. Based on a review of the current na-tech literature, this article illustrates a risk assessment method as a supporting tool for land use planning strategies aimed at reducing na-tech risk in urban areas. More specifically, a multi attribute decision-making method, combined with fuzzy techniques, has been developed. The method allows planners to take into account, according to different territorial units, all the individual na-tech risk factors, measured through both quantitative and qualitative parameters, while providing them with a na-tech risk index, useful to rank the territorial units and to single out the priority intervention areas. The method is designed to process information generally available about hazardous plants (safety reports), natural hazards (hazard maps) and features of urban systems mainly influencing their exposure and vulnerability to na-tech events (common statistical territorial data). Furthermore, the method implemented into a GIS framework should easily provide planners with comparable maps to figure out the hazard factors and the main territorial features influencing the exposure and vulnerability of urban systems to na-tech events. The method has been tested on a middle-sized Municipality in the Campania Region, identified as 2nd class seismic zone, according to the Ordinance 3274/2003, in which a LPG storage plant, classified as a plant with major accident potential by the Seveso II Directive (art. 9), is located just within the city core.

Aluminum toxicity is the main factor limiting the productivity of crop plants in acid soils, particularly in the tropics and subtropics. In this study, a doubled-haploid population derived from the rice (Oryza sativa L.) breeding lines CT9993 and IR62266 was used to map genes controlling Al tolerance. A genetic linkage map consisting of 280 DNA markers (RFLP, AFLP and SSR) was constructed to determine the position and nature of quantitative trait loci (QTLs) affecting Al tolerance. Three characters – control root length (CRL), Al-stressed root length (SRL) and root length ratio (RR) – were evaluated for the DH lines and the parents at the seedling stage in nutrient solution. A total of 20 QTLs controlling root growth under Al stress and control conditions were detected and distributed over 10 of the 12 rice chromosomes, reflecting multigenic control of these traits. The two QTLs of largest effect, qALRR-1-1 and qALRR-8 for root length ratio (a measurement of Al tolerance) were localized on chromosomes 1 and 8, respectively. Three other QTLs in addition to qALRR-8 were apparently unique in the CT9993 × IR62266 mapping population, which may explain the high level of Al tolerance in CT9993. Comparative mapping identified a conserved genomic region on chromosome 1 associated with Al tolerance across three rice genetic backgrounds. This region provides an important starting point for isolating genes responsible for different mechanisms of aluminum tolerance and understanding the genetic nature of this trait in rice and other cereals.

There is limited genetic mapping data useful for breeding programs of watermelon. Introgression lines should be a use-
ful tool for genetic studies and genetic enhancement of watermelon cultivars. In this study, we used an advanced re-
combinant population (BC2F2) to identify and map chromosomal segments of the wild watermelon Citrullus lanatus var. citroides that were incorporated in the genome of the watermelon cultivar Crimson Sweet (Citrullus lanatus var. lana-
tus). An advanced recombinant population (BC2F2) was constructed using a United States Plant Introduction (PI)
494817 (C. lanatus var. citroides) (known to have moderate resistance to bacterial fruit blotch) as a donor parent, and
the elite watermelon cultivar Crimson Sweet (C. lanatus var. lanatus) as the recurrent parent. The genetic linkage map
consists of 272 markers, including 89 sequence-related amplified polymorphism (SRAP), 72 targeted region amplifica-
tion polymorphism (TRAP), and 111 high frequency oligonucleotide-targeting active gene (HFO-TAG) markers. The
272 markers were assembled into 51 linkage groups, covering a total genetic distance of 2162 cM, with an average
genetic distance of 7.9 cM between markers. Also, we expended the genetic linkage map for watermelon derived from a testcross population {Griffin 14113 [C. lanatus var. citroide (L.H. Bailey) Mansf.] x watermelon cultivar New Hamp-
shire Midget (C. lanatus var. lanatus)} x PI 386015 [C. colocynthis (L.) Schrad.]. The genetic linkage map based on the
test cross population consists of 558 markers that cover a genetic distance of 2760.8 cM. This linkage map consists of
41 linkage group, including 10 large linkage groups (ranging from102-240 cM), nine intermediate size linkage groups
(ranging from 62-93 cM), and 22 small linkage groups (ranging from 2-56 cM). Comparative mapping between these
two linkage maps identified high consensus in 25 HFO-TAG markers and one TRAP marker that represent 8 linkage
groups in the BC2F2 population and 9 linkage groups in the testcross population. These results indicate that HFO-TAG
markers should be useful in comparative mapping. The extended genetic maps and the genetic population in this study
should be useful in breeding programs using marker assisted selection and should serve as a platform for further de-
velopment of introgression lines for watermelon.

We screened for simple sequence repeats (SSRs) found in ESTs derived from an EST-database development project ('Marine Genomics Europe' Network of Excellence). Different motifs of di-, tri-, tetra-, penta- and hexanucleotide SSRs were evaluated for variation in length and position in the expressed sequences, relative abundance and distribution in gilthead sea bream (Sparus aurata). We found 899 ESTs that harbor 997 SSRs (4.94%). On average, one SSR was found per 2.95 kb of EST sequence and the dinucleotide SSRs are the most abundant accounting for 47.6% of the total number. EST-SSRs were used as template for primer design. 664 primer pairs could be successfully identified and a subset of 206 pairs of primers was synthesized, PCR-tested and visualized on ethidium bromide stained agarose gels. The main objective was to further assess the potential of EST-SSRs as informative markers and investigate their cross-species amplification in sixteen teleost fish species: seven spari...

A novel approach is used in studying the error fields in the heliac facility "H-lNF. in the plasma Research Laboratory of the Australian National University by an electron beam mapping technique using a rotating multi-wire grid collector and a reconstruction technique developed in tomography known as Algebraic Reconstruction Technique (ART). Some error fields in H-INF are identified by comparing maps

A comprehensive genetic linkage map of the porcine genome has been developed by typing 128 genetic markers in a cross between the European Wild Boar and a domestic breed (Large White). The marker set includes 68 polymerase chain reaction-formatted microsatellites, 60 anchored reference markers in- formative for comparative mapping and 47 markers which have been physically assigned by in situ

Brassica napus (AACC genome) is an important oilseed crop that was formed by the fusion of the diploids B. rapa (AA) and B. oleracea (CC). The complete genomic sequence of the Brassica A genome will be available soon from the B. rapa genome sequencing project, but it is not clear how informative the A genome sequence in B. rapa (Ar) will be for predicting the structure and function of the A subgenome in the allotetraploid Brassica species B. napus (An). In this paper, we report the results of structural and functional comparative mapping between the A subgenomes of B. napus and B. rapa based on genetic maps that were anchored with bacterial artificial chromosomes (BACs)-sequence of B. rapa. We identified segmental conservation that represented by syntenic blocks in over one third of the A genome; meanwhile, comparative mapping of quantitative trait loci for seed quality traits identified a dozen homologous regions with conserved function in the A genome of the two species. However, several genomic rearrangement events, such as inversions, intra- and inter-chromosomal translocations, were also observed, covering totally at least 5% of the A genome, between allotetraploid B. napus and diploid B. rapa. Based on these results, the A genomes of B. rapa and B. napus are mostly functionally conserved, but caution will be necessary in applying the full sequence data from B. rapa to the B. napus as a result of genomic rearrangements in the A genome between the two species.