Gene pools and the genetic architecture of domesticated cowpea

Open Access JournalCowpea [Vigna unguiculata (L.) Walp.] is a major tropical legume crop grown in warm to hot areas throughout the world and especially important to the people of sub-Saharan Africa where the crop was domesticated. To date, relatively little is understood about its domestication origins and patterns of genetic variation. In this study, a worldwide collection of cowpea landraces and African ancestral wild cowpea was genotyped with more than 1200 single nucleotide polymorphism markers. Bayesian inference revealed the presence of two major gene pools in cultivated cowpea in Africa. Landraces from gene pool 1 are mostly distributed in western Africa while the majority of gene pool 2 are located in eastern Africa. Each gene pool is most closely related to wild cowpea in the same geographic region, indicating divergent domestication processes leading to the formation of two gene pools. The total genetic variation within landraces from countries outside Africa was slightly greater than within African landraces. Accessions from Asia and Europe were more related to those from western Africa while accessions from the Americas appeared more closely related to those from eastern Africa. This delineation of cowpea germplasm into groups of genetic relatedness will be valuable for guiding introgression efforts in breeding programs and for improving the efficiency of germplasm managemen

A multi-parent advanced generation inter-cross (MAGIC) population for genetic analysis and improvement of cowpea (Vigna unguiculata L. Walp.)

Published online: 21 Jan 2018Multi‐parent advanced generation inter‐cross (MAGIC) populations are an emerging type of resource for dissecting the genetic structure of traits and improving breeding populations. We developed a MAGIC population for cowpea (Vigna unguiculata L. Walp.) from eight founder parents. These founders were genetically diverse and carried many abiotic and biotic stress resistance, seed quality and agronomic traits relevant to cowpea improvement in the United States and sub‐Saharan Africa, where cowpea is vitally important in the human diet and local economies. The eight parents were inter‐crossed using structured matings to ensure that the population would have balanced representation from each parent, followed by single‐seed descent, resulting in 305 F8 recombinant inbred lines each carrying a mosaic of genome blocks contributed by all founders. This was confirmed by single nucleotide polymorphism genotyping with the Illumina Cowpea Consortium Array. These lines were on average 99.74% homozygous but also diverse in agronomic traits across environments. Quantitative trait loci (QTLs) were identified for several parental traits. Loci with major effects on photoperiod sensitivity and seed size were also verified by biparental genetic mapping. The recombination events were concentrated in telomeric regions. Due to its broad genetic base, this cowpea MAGIC population promises breakthroughs in genetic gain, QTL and gene discovery, enhancement of breeding populations and, for some lines, direct releases as new varieties

Variability of marine climate on the North Icelandic Shelf in a 1357-year proxy archive based on growth increments in the bivalve Arctica islandica

A multicentennial and absolutely-dated shell-based chronology for the marine environment of the North Icelandic Shelf has been constructed using annual growth increments in the shell of the long-lived bivalve clam Arctica islandica. The region from which the shells were collected is close to the North Atlantic Polar Front and is highly sensitive to the varying influences of Atlantic and Arctic water masses. A strong common environmental signal is apparent in the increment widths, and although the correlations between the growth increment indices and regional sea surface temperatures are significant at the 95% confidence level, they are low (r ~ 0.2), indicating that a more complex combination of environmental forcings is driving growth. Remarkable longevities of individual animals are apparent in the increment-width series used in the chronology, with several animals having lifetimes in excess of 300 years and one, at 507 years, being the longest-lived non-colonial animal so far reported whose age at death can be accurately determined. The sample depth is at least three shells after AD 1175, and the time series has been extended back to AD 649 with a sample depth of one or two by the addition of two further series, thus providing a 1357-year archive of dated shell material. The statistical and spectral characteristics of the chronology are investigated by using two different methods of removing the age-related trend in shell growth. Comparison with other proxy archives from the same region reveals several similarities in variability on multidecadal timescales, particularly during the period surrounding the transition from the Medieval Climate Anomaly to the Little Ice Age

Long-term stability of δ13C with respect to biological age in the aragonite shell of mature speciments of the bivalve mollusk Arctica islandica.

The stable carbon isotope ratio in bivalve shells (δ13CS) is an enigmatic geochemical archive whose interpretation is often frustrated by the intrusion of variable and unpredictable vital effects which can influence the mix of metabolic and dissolved inorganic carbon (DIC) in the shell material. The impacts of vital effects and rapid changes in calcification rates on the variability and value of δ13CS have been described in a number of studies and in many bivalve species with typical lifespans between a few years and a few decades, δ13CS has been observed to change (usually decreasing) with biological age. Very long-lived animals, by contrast, spend most of their lives in the mature, slow-growing phase, and it might be expected that in these instances the effect of changes in calcification rates on δ13CS would be less marked, or even absent. Analysis of δ13CS in mature (>40years old) Arctica islandica, reported here, indicates that this is the case. δ13CS in shell samples with biological ages between 42 and 391 years from four distinct sites in the North Atlantic shelf seas (Gulf of Maine, north Icelandic shelf, Irish Sea and North Sea) shows no age-related trend. This suggests that metabolic vital effects in mature A. islandica may be reasonably stable at the population level. If the drivers of isotopic disequilibrium between shell and ambient environment can be identified and quantified, it may be feasible to adjust for them and use δ13CS in mature A. islandica to investigate long-term changes in nutrient sources and as a robust proxy for δ13C of environmental DIC

Continuous marine radiocarbon reservoir calibration and the ¹³C Suess effect in the Irish Sea: results from the first multi-centennial shell-based marine master chronology

The identification in various proxy records of periods of rapid (decadal scale) climate change over recent millennia, together with the possibility that feedback mechanisms may amplify climate system responses to increasing atmospheric CO<sub>2</sub>, highlights the importance of a detailed understanding, at high spatial and temporal resolutions, of forcings and feedbacks within the system. Such an understanding has hitherto been limited because the temperate marine environment has lacked an absolute timescale of the kind provided by tree-rings for the terrestrial environment and by corals for the tropical marine environment. Here we present the first annually resolved, multi-centennial (489-year), absolutely dated, shell-based marine master chronology. The chronology has been constructed by detrending and averaging annual growth increment widths in the shells of multiple specimens of the very long-lived bivalve mollusc Arctica islandica, collected from sites to the south and west of the Isle of Man in the Irish Sea. The strength of the common environmental signal expressed in the chronology is fully comparable with equivalent statistics for tree-ring chronologies. Analysis of the <sup>14</sup>C signal in the shells shows no trend in the marine radiocarbon reservoir correction (ΔR), although it may be more variable before ∼ 1750. The δ<sup>13</sup>C signal shows a very significant (R2 = 0.456, p < 0.0001) trend due to the 13C Suess effect

Biharmonic surfaces in pseudo Euclidean spaces

Marine radiocarbon bomb-pulse time histories of annually resolved archives from temperate regions have been underexploited. We present here series of Delta C-14 excess from known-age annual increments of the long-lived bivalve mollusk Arctica islandica from 4 sites across the coastal North Atlantic (German Bight, North Sea; Tromso, north Norway; Siglufjordur, north Icelandic shelf; Grimsey, north Icelandic shelf) combined with published series from Georges Bank and Sable Bank (NW Atlantic) and the Oyster Ground (North Sea). The atmospheric bomb pulse is shown to be a step-function whose response in the marine environment is immediate but of smaller amplitude and which has a longer decay time as a result of the much larger marine carbon reservoir. Attenuation is determined by the regional hydrographic setting of the sites, vertical mixing, processes controlling the isotopic exchange of C-14 at the air-sea boundary, C-14 content of the freshwater flux, primary productivity, and the residence time of organic matter in the sediment mixed layer. The inventories form a sequence from high magnitude-early peak (German Bight) to low magnitude-late peak (Grimsey). All series show a rapid response to the increase in atmospheric Delta C-14 excess but a slow response to the subsequent decline resulting from the succession of rapid isotopic air-sea exchange followed by the more gradual isotopic equilibration in the mixed layer due to the variable marine carbon reservoir and incorporation of organic carbon from the sediment mixed layer. The data constitute calibration series for the use of the bomb pulse as a high-resolution dating tool in the marine environment and as a tracer of coastal ocean water masses

An improved consensus genetic linkage map of cowpea ( Vigna unguiculata L. Walp. )

Consensus genetic linkage maps are formed from merging individual linkage maps. They provide powerful tools for genetic analysis and a foundation for marker-assisted breeding, trait mapping, and positional cloning. In 2009, the first cowpea consensus map was developed. It included 928 markers spanning 11 linkage groups over a total map size of 680 centimorgans (cM), a 0.73 cM average marker distance. The map was the result of merging maps from 6 RIL populations genotyped with a 1536-SNP multiplexed assay developed from EST-derived genic SNPs. Here we report improvements to the consensus map for cowpea that result from merging genotype data from a total of 1070 lines composed of eight RIL and two F4 breeding populations. Individual maps were first constructed and then merged to develop a consensus map. The improved map is 680 cM in length and contains 1043 markers, which is an addition of 115 markers and an average 0.65 cm between markers. The map resolution is also increased with more marker bins, and there were some adjustments to marker order. The current SNP-based cowpea linkage map is included in a publicly available browser called HarvEST:Cowpea, which can be downloaded as a Windows software from http://harvest.ucr.edu or viewed through an online portal www.harvest-web.org