Production of haploids and doubled haploids in oil palm

Background: Oil palm is the world’s most productive oil-food crop despite yielding well below its theoretical maximum. This maximum could be approached with the introduction of elite F1 varieties. The development of such elite lines has thus far been prevented by difficulties in generating homozygous parental types for F1 generation. Results: Here we present the first high-throughput screen to identify spontaneously-formed haploid (H) and doubled haploid (DH) palms. We secured over 1,000 Hs and one DH from genetically diverse material and derived further DH/mixoploid palms from Hs using colchicine. We demonstrated viability of pollen from H plants and expect to generate 100% homogeneous F1 seed from intercrosses between DH/mixoploids once they develop female inflorescences. Conclusions: This study has generated genetically diverse H/DH palms from which parental clones can be selected in sufficient numbers to enable the commercial-scale breeding of F1 varieties. The anticipated step increase in productivity may help to relieve pressure to extend palm cultivation, and limit further expansion into biodiverse rainforest

Incidence of HIV and hepatitis C virus among people who inject drugs, and associations with age and sex or gender: a global systematic review and meta-analysis

BACKGROUND: Measuring the incidence of HIV and hepatitis C virus (HCV) infection among people who inject drugs (PWID) is key to track progress towards elimination. We aimed to summarise global data on HIV and primary HCV incidence among PWID and associations with age and sex or gender.METHODS: In this systematic review and meta-analysis, we updated an existing database of HIV and HCV incidence studies among PWID by searching MEDLINE, Embase, and PsycINFO, capturing studies published between Jan 1, 2000, and Dec 12, 2022, with no language or study design restrictions. We contacted authors of identified studies for unpublished or updated data. We included studies that estimated incidence by longitudinally re-testing people at risk of infection or by using assays for recent infection. We pooled incidence and relative risk (RR; young [generally defined as ≤25 years] vs older PWID; women vs men) estimates using random-effects meta-analysis and assessed risk of bias with a modified Newcastle-Ottawa scale. This study is registered with PROSPERO, CRD42020220884.FINDINGS: Our updated search identified 9493 publications, of which 211 were eligible for full-text review. An additional 377 full-text records from our existing database and five records identified through cross-referencing were assessed. Including 28 unpublished records, 125 records met the inclusion criteria. We identified 64 estimates of HIV incidence (30 from high-income countries [HICs] and 34 from low-income or middle-income countries [LMICs]) and 66 estimates of HCV incidence (52 from HICs and 14 from LMICs). 41 (64%) of 64 HIV and 42 (64%) of 66 HCV estimates were from single cities rather than being multi-city or nationwide. Estimates were measured over 1987-2021 for HIV and 1992-2021 for HCV. Pooled HIV incidence was 1·7 per 100 person-years (95% CI 1·3-2·3; I 2=98·4%) and pooled HCV incidence was 12·1 per 100 person-years (10·0-14·6; I 2=97·2%). Young PWID had a greater risk of HIV (RR 1·5, 95% CI 1·2-1·8; I 2=66·9%) and HCV (1·5, 1·3-1·8; I 2=70·6%) acquisition than older PWID. Women had a greater risk of HIV (RR 1·4, 95% CI 1·1-1·6; I 2=55·3%) and HCV (1·2, 1·1-1·3; I 2=43·3%) acquisition than men. For both HIV and HCV, the median risk-of-bias score was 6 (IQR 6-7), indicating moderate risk. INTERPRETATION: Although sparse, available HIV and HCV incidence estimates offer insights into global levels of HIV and HCV transmission among PWID. Intensified efforts are needed to keep track of the HIV and HCV epidemics among PWID and to expand access to age-appropriate and gender-appropriate prevention services that serve young PWID and women who inject drugs.FUNDING: Canadian Institutes of Health Research, Fonds de recherche du Québec-Santé, Canadian Network on Hepatitis C, UK National Institute for Health and Care Research, and WHO.</p

HRM curve profiles from a titration of maize + cowpea flour mixtures.

<p>Normalised High Resolution Melting (HRM) analysis of <i>rbcL</i> amplicons generated from template DNA extractions from ground flour of maize and cowpea grain according to the titration series: 0, 5, 10, 30, 50, 70, 90, 95 and 100% maize grains (in cowpea grains). <b>(A)</b> Normalised HRM curves of DNA from each of the ground seed mixtures. (<b>B)</b> Linear regression for HRM profile of cowpea and maize seed flour mixes at a melt temperature of 84.1^°C. Error bars represent the standard error of the mean. Linear regression of samples containing >50% maize can be described by the relationship y = 0.2984x + 17.964 and has an R² value of 0.9716.</p

Relationship between aerosol particle profile and sampling position as well as DNA isolated from pure maize and cowpea.

<p>(<b>A)</b> Decay of airborne tissue (non-starch) and starch particles at various heights above bins containing maize and cowpea grains. Error bars represent 2x standard deviation. (<b>B)</b> Concentration of maize and cowpea DNA recovered from aerosol samples collected at different sampling heights (H) in cm from grain bins containing maize or cowpea grains. Error bars indicate 2x standard deviation and account for 95% of variation. (<b>C)</b> Concentration of maize and cowpea DNA recovered from aerosol samples collected at different sampling distances (in cm) from grain bins containing maize or cowpea grains. Error bars indicate 2x standard deviation and account for 95% of variation.</p

HRM profiles from aerosol samples above a titration of maize + cowpea seed mixtures.

<p>High Resolution Melting (HRM) analysis of <i>rbcL</i> amplicons generated from template DNA extractions recovered from aerosol samples collected 10cm above 10kg grain bins containing 0%, 5%, 10%, 30%, 50%, 70%, 90%, 95% and 100% of maize grains with cowpea grains. (<b>A</b>)Normalised HRM curves of aerosol samples collected above each part of the grain mixture titration series. (<b>B)</b> Linear regression for normalised HRM profile of all aerosol samples collected 10cm height above grain bins at a melt temperature of 83.5^°C. Error bars represent standard error of the mean.</p

Species-specific minibarcode frequencies from aerosol samples collected above a titration of maize + cowpea seed mixtures.

<p>Frequency of maize and cowpea-specific mini-barcode sequences recovered from aerosol samples collected above individual grain bins in a titration series containing 0%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% and 100% (Coriolis samples) and 0%, 5%, 10%, 30%, 50%, 70%, 90%, 95% and 100% (vacuum samples) of maize grains in cowpea grains. (<b>A)</b> Histogram of the relative percentage of maize and cowpea mini-barcode sequences recovered from aerosol samples collected using a Coriolis aerosol sampler 60cm above bins representing the titration series of grain mixes. (<b>B)</b> Histogram of the relative percentage of maize and cowpea mini-barcode sequences recovered from aerosol samples collected using a hand-held, high power vacuum sampler 10cm above bins representing the titration series of grain mixes.</p

High-resolution melt analysis to identify and map sequence-tagged site anchor points onto linkage maps: a white lupin (Lupinus albus) map as an exemplar

THE provision of sequence-tagged site (STS) anchor points allows meaningful comparisons between mapping studies but can be a time-consuming process for nonmodel species or orphan crops. HERE, the first use of high-resolution melt analysis (HRM) to generate STS markers for use in linkage mapping is described. This strategy is rapid and low-cost, and circumvents the need for labelled primers or amplicon fractionation. USING white lupin (Lupinus albus, x = 25) as a case study, HRM analysis was applied to identify 91 polymorphic markers from expressed sequence tag (EST)-derived and genomic libraries. Of these, 77 generated STS anchor points in the first fully resolved linkage map of the species. The map also included 230 amplified fragment length polymorphisms (AFLP) loci, spanned 1916 cM (84.2% coverage) and divided into the expected 25 linkage groups. QUANTITATIVE trait loci (QTL) analyses performed on the population revealed genomic regions associated with several traits, including the agronomically important time to flowering (tf), alkaloid synthesis and stem height (Ph). Use of HRM-STS markers also allowed us to make direct comparisons between our map and that of the related crop, Lupinus angustifolius, based on the conversion of RFLP, microsatellite and single nucleotide polymorphism (SNP) markers into HRM markers.Adam E. Croxford, Tom Rogers, Peter D. S. Caligari and Michael J. Wilkinso