Identification of candidate genes and molecular markers for heat-induced brown discoloration of seed coats in cowpea [Vigna unguiculata (L.) Walp].

BackgroundHeat-induced browning (Hbs) of seed coats is caused by high temperatures which discolors the seed coats of many legumes, affecting the visual appearance and quality of seeds. The genetic determinants underlying Hbs in cowpea are unknown.ResultsWe identified three QTL associated with the heat-induced browning of seed coats trait, Hbs-1, Hbs-2 and Hbs-3, using cowpea RIL populations IT93K-503-1 (Hbs positive) x CB46 (hbs negative) and IT84S-2246 (Hbs positive) x TVu14676 (hbs negative). Hbs-1 was identified in both populations, accounting for 28.3% -77.3% of the phenotypic variation. SNP markers 1_0032 and 1_1128 co-segregated with the trait. Within the syntenic regions of Hbs-1 in soybean, Medicago and common bean, several ethylene forming enzymes, ethylene responsive element binding factors and an ACC oxidase 2 were observed. Hbs-1 was identified in a BAC clone in contig 217 of the cowpea physical map, where ethylene forming enzymes were present. Hbs-2 was identified in the IT93K-503-1 x CB46 population and accounted for of 9.5 to 12.3% of the phenotypic variance. Hbs-3 was identified in the IT84S-2246 x TVu14676 population and accounted for 6.2 to 6.8% of the phenotypic variance. SNP marker 1_0640 co-segregated with the heat-induced browning phenotype. Hbs-3 was positioned on BAC clones in contig512 of the cowpea physical map, where several ACC synthase 1 genes were present.ConclusionThe identification of loci determining heat-induced browning of seed coats and co-segregating molecular markers will enable transfer of hbs alleles into cowpea varieties, contributing to higher quality seeds

Genetic mapping and legume synteny of aphid resistance in African cowpea (Vigna unguiculata L. Walp.) grown in California.

The cowpea aphid Aphis craccivora Koch (CPA) is a destructive insect pest of cowpea, a staple legume crop in Sub-Saharan Africa and other semiarid warm tropics and subtropics. In California, CPA causes damage on all local cultivars from early vegetative to pod development growth stages. Sources of CPA resistance are available in African cowpea germplasm. However, their utilization in breeding is limited by the lack of information on inheritance, genomic location and marker linkage associations of the resistance determinants. In the research reported here, a recombinant inbred line (RIL) population derived from a cross between a susceptible California blackeye cultivar (CB27) and a resistant African breeding line (IT97K-556-6) was genotyped with 1,536 SNP markers. The RILs and parents were phenotyped for CPA resistance using field-based screenings during two main crop seasons in a 'hotspot' location for this pest within the primary growing region of the Central Valley of California. One minor and one major quantitative trait locus (QTL) were consistently mapped on linkage groups 1 and 7, respectively, both with favorable alleles contributed from IT97K-556-6. The major QTL appeared dominant based on a validation test in a related F2 population. SNP markers flanking each QTL were positioned in physical contigs carrying genes involved in plant defense based on synteny with related legumes. These markers could be used to introgress resistance alleles from IT97K-556-6 into susceptible local blackeye varieties by backcrossing

Biological and climate controls on North Atlantic marine carbon dynamics over the last millennium: Insights from an absolutely-dated shell based record from the North Icelandic Shelf

Given the rapid increase in atmospheric carbon dioxide concentrations (pCO2) over the industrial era, there is a pressing need to construct long‐term records of natural carbon cycling prior to this perturbation and to develop a more robust understanding of the role the oceans play in the sequestration of atmospheric carbon. Here we reconstruct the past biological and climate controls on the carbon isotopic (δ13Cshell) composition of the North Icelandic shelf waters over the last millennium, derived from the shells of the long‐lived marine bivalve mollusk Arctica islandica. Variability in the annually resolved δ13Cshell record is dominated by multidecadal variability with a negative trend (−0.003 ± 0.002‰ yr−1) over the industrial era (1800–2000 Common Era). This trend is consistent with the marine Suess effect brought about by the sequestration of isotopically light carbon (δ13C of CO2) derived from the burning of fossil fuels. Comparison of the δ13Cshell record with Contemporaneous proxy archives, over the last millennium, and instrumental data over the twentieth century, highlights that both biological (primary production) and physical environmental factors, such as relative shifts in the proportion of Subpolar Mode Waters and Arctic Intermediate Waters entrained onto the North Icelandic shelf, atmospheric circulation patterns associated with the winter North Atlantic Oscillation, and sea surface temperature and salinity of the subpolar gyre, are the likely mechanisms that contribute to natural variations in seawater δ13C variability on the North Icelandic shelf. Contrasting δ13C fractionation processes associated with these biological and physical mechanisms likely cause the attenuated marine Suess effect signal at this locality

ParentChecker: a computer program for automated inference of missing parental genotype calls and linkage phase correction

<p>Abstract</p> <p>Background</p> <p>Accurate genetic maps are the cornerstones of genetic discovery, but their construction can be hampered by missing parental genotype information. Inference of parental haplotypes and correction of phase errors can be done manually on a one by one basis with the aide of current software tools, but this is tedious and time consuming for the high marker density datasets currently being generated for many crop species. Tools that help automate the process of inferring parental genotypes can greatly speed the process of map building. We developed a software tool that infers and outputs missing parental genotype information based on observed patterns of segregation in mapping populations. When phases are correctly inferred, they can be fed back to the mapping software to quickly improve marker order and placement on genetic maps.</p> <p>Results</p> <p>ParentChecker is a user-friendly tool that uses the segregation patterns of progeny to infer missing genotype information of parental lines that have been used to construct a mapping population. It can also be used to automate correction of linkage phase errors in genotypic data that are in ABH format.</p> <p>Conclusion</p> <p>ParentChecker efficiently improves genetic mapping datasets for cases where parental information is incomplete by automating the process of inferring missing genotypes of inbred mapping populations and can also be used to correct linkage phase errors in ABH formatted datasets.</p

Experimental Determination of Salinity, Temperature, Growth, and Metabolic Effects on Shell Isotope Chemistry of Mytilus Edulis Collected from Maine and Greenland

To study the effects of temperature, salinity, and life processes (growth rates, size, metabolic effects, and physiological/ genetic effects) on newly precipitated bivalve carbonate, we quantified shell isotopic chemistry of adult and juvenile animals of the intertidal bivalve Mytilus edulis (Blue mussel) collected alive from western Greenland and the central Gulf of Maine and cultured them under controlled conditions. Data for juvenile and adult M. edulis bivalves cultured in this study, and previously by Wanamaker et al. (2006), yielded statistically identical paleotemperature relationships. On the basis of these experiments we have developed a species-specific paleotemperature equation for the bivalve M. edulis [T degrees C = 16.28 (+/- 0.10) -4.57 (+/- 0.15) {delta(18)O(c) VPBD - delta(18)O(w) VSMOW} + 0.06 (+/- 0.06) {delta(18)O(c) VPBD - delta(18)O(w) VSMOW}(2); r(2) = 0.99; N = 323; p \u3c 0.0001]. Compared to the Kim and O\u27Neil (1997) inorganic calcite equation, M. edulis deposits its shell in isotope equilibrium (delta(18)O(calcite)) with ambient water. Carbon isotopes (delta(13)C(calcite)) from sampled shells were substantially more negative than predicted values, indicating an uptake of metabolic carbon into shell carbonate, and delta(13)C(calcite) disequilibrium increased with increasing salinity. Sampled shells of M. edulis showed no significant trends in delta(18)O(calcite) based on size, cultured growth rates, or geographic collection location, suggesting that vital effects do not affect delta(18)O(calcite) in M. edulis. The broad modern and paleogeographic distribution of this bivalve, its abundance during the Holocene, and the lack of an intraspecies physiologic isotope effect demonstrated here make it an ideal nearshore paleoceanographic proxy throughout much of the North Atlantic Ocean

Detection and validation of single feature polymorphisms in cowpea (Vigna unguiculata L. Walp) using a soybean genome array

<p>Abstract</p> <p>Background</p> <p>Cowpea (<it>Vigna unguiculata </it>L. Walp) is an important food and fodder legume of the semiarid tropics and subtropics worldwide, especially in sub-Saharan Africa. High density genetic linkage maps are needed for marker assisted breeding but are not available for cowpea. A single feature polymorphism (SFP) is a microarray-based marker which can be used for high throughput genotyping and high density mapping.</p> <p>Results</p> <p>Here we report detection and validation of SFPs in cowpea using a readily available soybean (<it>Glycine max) </it>genome array. Robustified projection pursuit (RPP) was used for statistical analysis using RNA as a surrogate for DNA. Using a 15% outlying score cut-off, 1058 potential SFPs were enumerated between two parents of a recombinant inbred line (RIL) population segregating for several important traits including drought tolerance, <it>Fusarium </it>and brown blotch resistance, grain size and photoperiod sensitivity. Sequencing of 25 putative polymorphism-containing amplicons yielded a SFP probe set validation rate of 68%.</p> <p>Conclusion</p> <p>We conclude that the Affymetrix soybean genome array is a satisfactory platform for identification of some 1000's of SFPs for cowpea. This study provides an example of extension of genomic resources from a well supported species to an orphan crop. Presumably, other legume systems are similarly tractable to SFP marker development using existing legume array resources.</p