The impact of transposable elements on the structure, evolution and function of the rice genome

Transposable elements (TEs) are ubiquitous in plants and are the primary genomic component of the majority of taxa. Knowledge of their impact on the structure, function and evolution of plant genomes is therefore a priority in the field of genomics. Rice, as one of the most prevalent crops for food security worldwide, has been subjected to intense research efforts over recent decades. Consequently, a considerable amount of genomic resources has been generated and made freely available to the scientific community. These can be exploited both to improve our understanding of some basic aspects of genome biology of this species and to develop new concepts for crop improvement. In this review, we describe the current knowledge on how TEs have shaped rice chromosomes and propose a new strategy based on a genome-wide association study (GWAS) to address the important question of their functional impact on this crop.

Yam genomics supports West Africa as a major cradle of crop domestication

While there has been progress in our understanding of the origin and history of agriculture in sub-Saharan Africa, a unified perspective is still lacking on where and how major crops were domesticated in the region. Here, we investigated the domestication of African yam (Dioscorea rotundata), a key crop in early African agriculture. Using whole-genome resequencing and statistical models, we show that cultivated yam was domesticated from a forest species. We infer that the expansion of African yam agriculture started in the Niger River basin. This result, alongside with the origins of African rice and pearl millet, supports the hypothesis that the vicinity of the Niger River was a major cradle of African agriculture.

Retrotranspositional landscape of Asian rice revealed by 3000 genomes

The recent release of genomic sequences for 3000 rice varieties provides access to the genetic diversity at species level for this crop. We take advantage of this resource to unravel some features of the retrotranspositional landscape of rice. We develop software TRACKPOSON specifically for the detection of transposable elements insertion polymorphisms (TIPs) from large datasets. We apply this tool to 32 families of retrotransposons and identify more than 50,000 TIPs in the 3000 rice genomes. Most polymorphisms are found at very low frequency, suggesting that they may have occurred recently in agro. A genome-wide association study shows that these activations in rice may be triggered by external stimuli, rather than by the alteration of genetic factors involved in transposable element silencing pathways. Finally, the TIPs dataset is used to trace the origin of rice domestication. Our results suggest that rice originated from three distinct domestication events.

Molecular basis of African yam domestication: analyses of selection point to root development, starch biosynthesis, and photosynthesis related genes

BACKGROUND

After cereals, root and tuber crops are the main source of starch in the human diet. Starch biosynthesis was certainly a significant target for selection during the domestication of these crops. But domestication of these root and tubers crops is also associated with gigantism of storage organs and changes of habitat.

RESULTS

We studied here, the molecular basis of domestication in African yam, Dioscorea rotundata. The genomic diversity in the cultivated species is roughly 30% less important than its wild relatives. Two percent of all the genes studied showed evidences of selection. Two genes associated with the earliest stages of starch biosynthesis and storage, the sucrose synthase 4 and the sucrose-phosphate synthase 1 showed evidence of selection. An adventitious root development gene, a SCARECROW-LIKE gene was also selected during yam domestication. Significant selection for genes associated with photosynthesis and phototropism were associated with wild to cultivated change of habitat. If the wild species grow as vines in the shade of their tree tutors, cultivated yam grows in full light in open fields.

CONCLUSIONS

Major rewiring of aerial development and adaptation for efficient photosynthesis in full light characterized yam domestication.

[Prevalence and determinants of hypertension in Lomé (Togo): results of a screening in May 2011]

BACKGROUND

The prevalence of hypertension in the Sub-Saharan Africa region is increasing as a manifestation of the epidemiological transition, and this fact will oblige these countries to mobilize significant resources. World Bank estimates cheaper to prevent cardiovascular disease than to treat people once these diseases are established suggesting the need to know the prevalence of hypertension in order to allow prevention programs in our population. However, data in Togolese populations are rare. The purpose of the present study was to determine the prevalence of high blood pressure and its risk factors in Lomé.

METHODS

We performed a cross-sectional survey among 2002 unselected respondents of the municipality of Lomé in May 2011. A questionnaire has been filled about family history of hypertension, habits and practices that affect hypertension on behalf of each respondent and anthropometric data and blood pressure has been measured.

RESULTS

The prevalence of high blood pressure was 36.7% (34.6% of male vs. 38.4% of female, OR=0.85; 95%CI=0.7-1.02; P=0.08); 42.4% of the hypertensive respondents have been diagnosed at the screening. Blood pressure was positively correlated to the age (SBP: r=+0.46; P=0.001; DBP: r=+0.36; P<0.001), the body mass index (SBP: r=+0.7; P<0.001; DBP: r=+0.89; P<0.001) and waist circumference (SBP: r=+0.28; P<0.001; DBP: r=+0.3; P<0.001). There was a significant relationship between arterial hypertension and obesity (OR=1.65; 95%CI=1.47-1.84; P=0.003), salt consumption (OR=1.4; 95%CI=1.13-1.72; P<0.001) and oral contraception (OR=2.1; 95%CI=1.29-3.43; P=0.002).

CONCLUSION

There was a high prevalence and low awareness of arterial hypertension in the municipality of Lomé with a female prevalence. This affection was correlated to age, salt consumption and obesity. This study raises the need for accentuating the prevention in our poor populations which are unable to face adverse outcomes which can occur.