Host–parasite coevolution can maintain high levels of genetic diversity in traits involved in species interactions. In many systems, host traits exploited by parasites are constrained by use in other functions, leading to complex selective pressures across space and time. Here, we study genome-wide variation in the staple crop Sorghum bicolor (L.) Moench and its association with the parasitic weed Striga hermonthica (Delile) Benth., a major constraint to food security in Africa. We hypothesize that geographic selection mosaics across gradients of parasite occurrence maintain genetic diversity in sorghum landrace resistance. Suggesting a role in local adaptation to parasite pressure, multiple independent loss-of-function alleles at sorghum LOW GERMINATION STIMULANT 1 (LGS1) are broadly distributed among African landraces and geographically associated with S. hermonthica occurrence. However, low frequency of these alleles within S. hermonthica-prone regions and their absence elsewhere implicate potential trade-offs restricting their fixation. LGS1 is thought to cause resistance by changing stereochemistry of strigolactones, hormones that control plant architecture and below-ground signaling to mycorrhizae and are required to stimulate parasite germination. Consistent with trade-offs, we find signatures of balancing selection surrounding LGS1 and other candidates from analysis of genome-wide associations with parasite distribution. Experiments with CRISPR–Cas9-edited sorghum further indicate that the benefit of LGS1-mediated resistance strongly depends on parasite genotype and abiotic environment and comes at the cost of reduced photosystem gene expression. Our study demonstrates long-term maintenance of diversity in host resistance genes across smallholder agroecosystems, providing a valuable comparison to both industrial farming systems and natural communities.
Sorghum (Sorghum bicolor L.) is a staple food crops in the arid and rainfed production ecologies. Sorghum plays a critical role in resilient farming and is projected as a smart crop to overcome the food and nutritional insecurity in the developing world. The development and characterisation of the sorghum pan-genome will provide insight into genome diversity and functionality, supporting sorghum improvement. We built a sorghum pan-genome using reference genomes as well as 354 genetically diverse sorghum accessions belonging to different races. We explored the structural and functional characteristics of the pan-genome and explain its utility in supporting genetic gain. The newly-developed pan-genome has a total of 35,719 genes, a core genome of 16,821 genes and an average of 32,795 genes in each cultivar. The variable genes are enriched with environment responsive genes and classify the sorghum accessions according to their race. We show that 53% of genes display presence-absence variation, and some of these variable genes are predicted to be functionally associated with drought adaptation traits. Using more than two million SNPs from the pan-genome, association analysis identified 398 SNPs significantly associated with important agronomic traits, of which, 92 were in genes. Drought gene expression analysis identified 1,788 genes that are functionally linked to different conditions, of which 79 were absent from the reference genome assembly. This study provides comprehensive genomic diversity resources in sorghum which can be used in genome assisted crop improvement.
This is a case-control study conducted to examine the risk factors for multidrug resistance (MDR) among patients with pulmonary tuberculosis (TB) in four centers in Burkina Faso, West Africa: Ouagadougou, Bobo-Dioulasso, Gorom-Gorom, and Dori. Fifty-six MDR-TB cases and 304 controls were enrolled of which 40 MDR-TB cases and 222 controls were from Ouagadougou. The majority of cases were male, with 39 among MDR-TB cases and 205 in controls. The MDR-TB cases were aged from 14 to 75 years versus 11 to 75 years in the controls. The total risk assessment battery score was 11. Living outside of Burkina Faso (adjusted odds ratio [OR] = 0.017; 95% confidence interval [95% CI]: 0.001-0.325), known TB contact (OR = 0.045; 95% CI: 0.004-0.543), and patients with previous history of TB treatment (OR = 0.004; 95% CI: 0.000-0.0.052) were significantly associated with MDR-TB. TB contact and mainly previous treatment were the strongest determinants of MDR-TB. Also, living outside Burkina was a risk factor.
Many farmers in West and Central Africa (WCA) prefer tall (>3 m) grain sorghum [Sorghum bicolor (L.) Moench] for various reasons. This study seeks to determine (i) what yield superiority newly bred, tall, photoperiod‐sensitive guinea‐race sorghum hybrids can provide relative to an adapted landrace variety across a wide range of productivity conditions, and (ii) the risk of these hybrids failing to provide yield superiority for individual farmers. Seven hybrids, one local check, and eight pure‐line progenies were evaluated in 37 farmer‐managed, on‐farm yield trials across three Malian zones and 3 yr. Environments were classified into four productivity groups (low [0.78–1.10 Mg ha−1], mid‐low [1.10–1.50 Mg ha−1], mid‐high [1.50–2.00 Mg ha−1] and high [2.00–2.65 Mg ha−1]) based on their trial mean grain yield. Mean yields of the seven tall hybrids were 3 to 17% (ranging from 0.06 to 0.28 Mg ha−1) higher than that of the local check across all environments and were highest (14–47%) averaged across the seven trials with the lowest mean yields. The individual overall highest‐yielding hybrid showed superiorities over the local check in the low, mid‐low, mid‐high, and high productivity levels of 0.43 (47%), 0.14 (10%), 0.47 (27%), and 0.34 (14%) Mg ha−1, respectively. The tall hybrids rarely had yields significantly inferior to the local check. Farmers’ preference for, and the possible benefits of, taller plant types may lead farmers to grow tall hybrids, particularly under the typical low‐productivity production conditions of WCA.
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