Identification and characterization of abundant repetitive sequences in Eragrostis tef cv. Enatite genome

Multiple alignment of Ty1-copia RT paralog sequences identified in teff cv Enantite and Tsedey. (MSF 51 kb

Correlation analysis of the transcriptome of growing leaves with mature leaf parameters in a maize RIL population

Background: To sustain the global requirements for food and renewable resources, unraveling the molecular networks underlying plant growth is becoming pivotal. Although several approaches to identify genes and networks involved in final organ size have been proven successful, our understanding remains fragmentary. Results: Here, we assessed variation in 103 lines of the Zea mays B73xH99 RIL population for a set of final leaf size and whole shoot traits at the seedling stage, complemented with measurements capturing growth dynamics, and cellular measurements. Most traits correlated well with the size of the division zone, implying that the molecular basis of final leaf size is already defined in dividing cells of growing leaves. Therefore, we searched for association between the transcriptional variation in dividing cells of the growing leaf and final leaf size and seedling biomass, allowing us to identify genes and processes correlated with the specific traits. A number of these genes have a known function in leaf development. Additionally, we illustrated that two independent mechanisms contribute to final leaf size, maximal growth rate and the duration of growth. Conclusions: Untangling complex traits such as leaf size by applying in-depth phenotyping allows us to define the relative contributions of the components and their mutual associations, facilitating dissection of the biological processes and regulatory networks underneath

Draft Whole-Genome Sequence of the Biocontrol Agent Trichoderma harzianum T6776

Trichoderma harzianum T6776 is a promising beneficial isolate whose effects consist of growth promotion, positive response of photosynthetic activity, hormonal signaling, and carbon partitioning in tomato, coupled with biocontrol of plant pathogens. Here, we present the first genome assembly of T6776, providing a useful platform for the scientific community

Traditional knowledge affects soil management ability of smallholder farmers in marginal areas

Soil fertility is key to sustainable intensification of agriculture and food security in sub-Saharan Africa. However, when soil nutrients are not adequately managed, smallholder farming practices slowly erode soils to almost inert systems. This case study contributes to the understanding of such failures in marginal areas. We integrate agronomic and social sciences approaches to explore links between smallholder households’ farming knowledge and soil fertility in an ethnopedological perspective. We interview 280 smallholder households in two areas of the Ethiopian highlands, while collecting measures of 11 soil parameters at their main field. By analyzing soil compositions at tested households, we identify a novel measure of soil management ability, which provides an effective empirical characterization of the soil managing capacity of a household. Regression analysis is used to evaluate the effects of household knowledge on the soil management ability derived from laboratory analysis. Results highlight the complexity of knowledge transmission in low-input remote areas. We are able to disentangle a home learning and a social learning dimension of the household knowledge and appraise how they can result in virtuous and vicious cycles of soil management ability. We show that higher soil management ability is associated with farmers relying to a great extent on farming knowledge acquired within the household, as a result of practices slowly elaborated over the years. Conversely, lower soil management ability is linked to households valuing substantially farming knowledge acquired through neighbors and social gatherings. The present study is the first to formulate the concept of soil management ability and to investigate the effects of the presence and the types of farming knowledge on the soil management ability of smallholder farmers in remote areas. We show that farming knowledge has a primary role on soil fertility and we advise its consideration in agricultural development policies

Integrating conventional and participatory crop improvement for smallholder agriculture using the seeds for needs approach: A review

In response to the climate change, it is essential to provide smallholder farmers with improved field crop genotypes that may increase the resilience of their farming system. This requires a fast turnover of varieties in a system capable of injecting significant amounts of genetic diversity into productive landscapes. Crop improvement is a pivotal strategy to cope with and adapt to climate change. Modern breeding may rely on the genomics revolution to speed up the development of new varieties with adaptive potential. However, centralized breeding may not adequately address smallholder farmers’ needs for more locally acclimatized varieties or groups of varieties. This, in turn, constrains adoption of new varieties that reduces the effectiveness of a resource-intensive breeding process, an issue that may be overcome with participatory, decentralized approaches. Whether high-tech centralized breeding or decentralized participatory approaches are better suited for smallholder farmers in the global South is hotly debated. Sidestepping any false dichotomies and ideological issues in these debates, this review provides a perspective on relevant advances in a breeding approach that combines the two approaches and uses genomics for trait mining from ex situ collections of genetic materials, participatory multilocation trials and crowdsourced citizen science. It argues that this new combination of high-tech centralized and participatory decentralized methods can provide a coherent and effective approach to breeding for climate adaptation and the present review advocates on a different way forward for the future research

miRVine: a microRNA expression atlas of grapevine based on small RNA sequencing

miRNAs are the most abundant class of small non-coding RNAs, and they are involved in post-transcriptional regulations, playing a crucial role in the refinement of genetic programming during plant development. Here we present a comprehensive picture of miRNA regulation in Vitis vinifera L. plant during its complete life cycle. Furthering our knowledge about the post-transcriptional regulation of plant development is fundamental to understand the biology of such an important crop

Genetic diversity and selection signatures in maize landraces compared across 50 years of in situ and ex situ conservation

Genomics-based, longitudinal comparisons between ex situ and in situ agrobiodiversity conservation strategies can contribute to a better understanding of their underlying effects. However, landrace designations, ambiguous common names, and gaps in sampling information complicate the identification of matching ex situ and in situ seed lots. Here we report a 50- year longitudinal comparison of the genetic diversity of a set of 13 accessions from the state of Morelos, Mexico, conserved ex situ since 1967 and retrieved in situ from the same donor families in 2017. We interviewed farmer families who donated in situ landraces to understand their germplasm selection criteria. Samples were genotyped by sequencing, producing 74,739 SNPs. Comparing the two sample groups, we show that ex situ and in situ genome-wide diversity was similar. In situ samples had 3.1% fewer SNPs and lower pairwise genetic distances (Fst 0.008–0.113) than ex situ samples (Fst 0.031–0.128), but displayed the same heterozygosity. Despite genome-wide similarities across samples, we could identify several loci under selection when comparing in situ and ex situ seed lots, suggesting ongoing evolution in farmer fields. Eight loci in chromosomes 3, 5, 6, and 10 showed evidence of selection in situ that could be related with farmers’ selection criteria surveyed with focus groups and interviews at the sampling site in 2017, including wider kernels and larger ear size. Our results have implications for ex situ collection resampling strategies and the in situ conservation of threatened landraces

Correction: High throughput approaches reveal splicing of primary microRNA transcripts and tissue specific expression of mature microRNAs in Vitis vinifera

The version of this article published in BMC Genomics 2009, 10:558, contains data in Table 1 which are now known to be unreliable, and an illustration, in Figure 1, of unusual miRNA processing events predicted by these unreliable data. In this full-length correction, new data replace those found to be unreliable, leading to a more straightforward interpretation without altering the principle conclusions of the study. Table 1 and associated methods have been corrected, Figure 1 deleted, supplementary file 1 added, and modifications made to the sections "Deep sequencing of small RNAs from grapevine leaf tissue" and "Microarray analysis of miRNA expression". The editors and authors regret the inconvenience caused to readers by premature publication of the original paper

High throughput approaches reveal splicing of primary microRNA transcripts and tissue specific expression of mature microRNAs in Vitis vinifera

<p>Abstract</p> <p>Background</p> <p>MicroRNAs are short (~21 base) single stranded RNAs that, in plants, are generally coded by specific genes and cleaved specifically from hairpin precursors. MicroRNAs are critical for the regulation of multiple developmental, stress related and other physiological processes in plants. The recent annotation of the genome of the grapevine (<it>Vitis vinifera </it>L.) allowed the identification of many putative conserved microRNA precursors, grouped into multiple gene families.</p> <p>Results</p> <p>Here we use oligonucleotide arrays to provide the first indication that many of these microRNAs show differential expression patterns between tissues and during the maturation of fruit in the grapevine. Furthermore we demonstrate that whole transcriptome sequencing and deep-sequencing of small RNA fractions can be used both to identify which microRNA precursors are expressed in different tissues and to estimate genomic coordinates and patterns of splicing and alternative splicing for many primary miRNA transcripts.</p> <p>Conclusion</p> <p>Our results show that many microRNAs are differentially expressed in different tissues and during fruit maturation in the grapevine. Furthermore, the demonstration that whole transcriptome sequencing can be used to identify candidate splicing events and approximate primary microRNA transcript coordinates represents a significant step towards the large-scale elucidation of mechanisms regulating the expression of microRNAs at the transcriptional and post-transcriptional levels.</p