Dissecting the genetic basis of drought responses in common bean using natural variation

The common bean (Phaseolus vulgaris L) is the most important legume for human consumption, contributing 30% of the total daily protein intake in developing countries. A major limitation for its cultivation is drought, which causes more than 60% of the annual losses. Among physiological adaptations to drought, delaying senescence and extending the photosynthetic capacity can improve crop productivity. This strategy is known as functional "stay-green" (SG) and has been discussed as a goal in plant breeding to alleviate the loss of yield under water scarcity conditions. The genetic components behind SG traits have been explored specially in cereals, but they are to date poorly studied in the common bean. For this, we screened 71 common bean cultivars belonging to the three most important gene-pools, Mesoamerica, Andes and Europe, selected to cover the natural variation of the species. Phenotyping experiments under terminal drought during long-days in greenhouse conditions, identified six photoperiod insensitive cultivars of European origin with a clear SG phenotype. Using SNP data produced from whole genome re-sequencing data, we obtained 10 variants significantly associated to the SG phenotype on chromosomes 1, 3, 7, 8, 9 and 10 that are in close proximity to gene models with functional annotations related to hormone signaling and anti-oxidant production. Calculating pairwise FST between subgroups of cultivars divided according to their drought response (susceptibility, escape, recovery or SG), we identified up to 29 genomic windows accounting for 1,45Mb that differentiate SG cultivars; these signals were especially strong on chromosomes 1, 5 and 10. Within these windows, we found genes directly involved in photosynthetic processes and trehalose synthesis. Altogether, these signals represent good targets for further characterization and highlight the multigenic nature of the SG response in legumes

Comparative Study of Pine Reference Genomes Reveals Transposable Element Interconnected Gene Networks

Sequencing the giga-genomes of several pine species has enabled comparative genomic analyses of these outcrossing tree species. Previous studies have revealed the wide distribution and extraordinary diversity of transposable elements (TEs) that occupy the large intergenic spaces in conifer genomes. In this study, we analyzed the distribution of TEs in gene regions of the assembled genomes of Pinus taeda and Pinus lambertiana using high-performance computing resources. The quality of draft genomes and the genome annotation have significant consequences for the investigation of TEs and these aspects are discussed. Several TE families frequently inserted into genes or their flanks were identified in both species' genomes. Potentially important sequence motifs were identified in TEs that could bind additional regulatory factors, promoting gene network formation with faster or enhanced transcription initiation. Node genes that contain many TEs were observed in multiple potential transposable element-associated networks. This study demonstrated the increased accumulation of TEs in the introns of stress-responsive genes of pines and suggests the possibility of rewiring them into responsive networks and sub-networks interconnected with node genes containing multiple TEs. Many such regulatory influences could lead to the adaptive environmental response clines that are characteristic of naturally spread pine populations

Comparative Study of Pine Reference Genomes Reveals Transposable Element Interconnected Gene Networks

Sequencing the giga-genomes of several pine species has enabled comparative genomic analyses of these outcrossing tree species. Previous studies have revealed the wide distribution and extraordinary diversity of transposable elements (TEs) that occupy the large intergenic spaces in conifer genomes. In this study, we analyzed the distribution of TEs in gene regions of the assembled genomes of Pinus taeda and Pinus lambertiana using high-performance computing resources. The quality of draft genomes and the genome annotation have significant consequences for the investigation of TEs and these aspects are discussed. Several TE families frequently inserted into genes or their flanks were identified in both species’ genomes. Potentially important sequence motifs were identified in TEs that could bind additional regulatory factors, promoting gene network formation with faster or enhanced transcription initiation. Node genes that contain many TEs were observed in multiple potential transposable element-associated networks. This study demonstrated the increased accumulation of TEs in the introns of stress-responsive genes of pines and suggests the possibility of rewiring them into responsive networks and sub-networks interconnected with node genes containing multiple TEs. Many such regulatory influences could lead to the adaptive environmental response clines that are characteristic of naturally spread pine populations

Dissecting the genetic basis of drought responses in common bean using natural variation

The common bean (Phaseolus vulgaris L) is the most important legume for human consumption, contributing 30% of the total daily protein intake in developing countries. A major limitation for its cultivation is drought, which causes more than 60% of the annual losses. Among physiological adaptations to drought, delaying senescence and extending the photosynthetic capacity can improve crop productivity. This strategy is known as functional “stay-green” (SG) and has been discussed as a goal in plant breeding to alleviate the loss of yield under water scarcity conditions. The genetic components behind SG traits have been explored specially in cereals, but they are to date poorly studied in the common bean. For this, we screened 71 common bean cultivars belonging to the three most important gene-pools, Mesoamerica, Andes and Europe, selected to cover the natural variation of the species. Phenotyping experiments under terminal drought during long-days in greenhouse conditions, identified six photoperiod insensitive cultivars of European origin with a clear SG phenotype. Using SNP data produced from whole genome re-sequencing data, we obtained 10 variants significantly associated to the SG phenotype on chromosomes 1, 3, 7, 8, 9 and 10 that are in close proximity to gene models with functional annotations related to hormone signaling and anti-oxidant production. Calculating pairwise FST between subgroups of cultivars divided according to their drought response (susceptibility, escape, recovery or SG), we identified up to 29 genomic windows accounting for 1,45Mb that differentiate SG cultivars; these signals were especially strong on chromosomes 1, 5 and 10. Within these windows, we found genes directly involved in photosynthetic processes and trehalose synthesis. Altogether, these signals represent good targets for further characterization and highlight the multigenic nature of the SG response in legumes

Adaptive introgression facilitate adaptation to high latitudes in European aspen (Populus tremula L.)

Understanding local adaptation has become a key research area given the ongoing climate challenge and the concomitant requirement to conserve genetic resources. Perennial plants, such as forest trees, are good models to study local adaptation given their wide geographic distribution, largely outcrossing mating systems and demographic histories. We evaluated signatures of local adaptation in European aspen (Populus tremula) across Europe by means of whole genome re-sequencing of a collection of 411 individual trees. We dissected admixture patterns between aspen lineages and observed a strong genomic mosaicism in Scandinavian trees, evidencing different colonization trajectories into the peninsula from Russia, Central and Western Europe. As a consequence of the secondary contacts between populations after the last glacial maximum (LGM), we detected an adaptive introgression event in a genome region of ∼500kb in chromosome 10, harboring a large-effect locus that has previously been shown to contribute to adaptation to the short growing seasons characteristic of northern Scandinavia. Demographic simulations and ancestry inference suggest an Eastern origin - probably Russian - of the adaptive Nordic allele which nowadays is present in a homozygous state at the north of Scandinavia. The strength of introgression and positive selection signatures in this region is a unique feature in the genome. Furthermore, we detected signals of balancing selection, shared across regional populations, that highlight the importance of standing variation as a primary source of alleles that facilitate local adaptation. Our results therefore emphasize the importance of migration-selection balance underlying the genetic architecture of key adaptive quantitative traits

Autogenic Training Relaxation Helping Postpartum Mothers to Achieve Successful Breastfeeding on Early Lactation Period

Introduction: The numbers of breastfeeding failures are mostly caused by mothers` disbelief to themselves. One method that can be done to overcome these problems in accordance with the self-care nursing theory is the autogenic training relaxation. This method teaches mothers to be self-sufficient in building a positive intention and motivation to help the process of breastfeeding. This study aimed to examine the influence of autogenic training relaxation to the effectiveness of breastfeeding and the enhancement of breast milk volume on maternal postpartum. Method: By using an experimental posttest only-non equivalent control group design, 26 samples were taken based on the criteria and divided into two groups by matching technuiqe. autogenic training was given through MP3 Player for 3 weeks. Post-test observation conducted on the third week by home visit. Via Christi Breastfeeding Assessment Tool Jan Riordan modifications used to assess the effectiveness of breastfeeding, and to measure the milk ejection volume, used weighing test using electronic baby scales. Data were analyzed using one-tailed independent t test with α ≤ 0.05. Result: The analysis showed that mothers who did autogenic training relaxation could breastfeed more effectively and had greater average volume of milk ejection than the control group (p = 0.000 and p = 0.001). Discussion: It can be concluded that autogenic relaxation training techniques affect the effectiveness of breastfeeding and breast milk volume. These results can be considered that autogenic training as an intervention in program of support for breastfeeding mothers

The advantage of parallel selection of domestication genes to accelerate crop improvement

Abstract A recent study identifies a locus controlling seed dormancy – a key trait of the ‘domestication syndrome’ – that has been selected for in parallel across multiple crop families

Genomic history of the origin and domestication of common bean unveils its closest sister species

Rendón-Anaya, Martha et. al.[Background] Modern civilization depends on only a few plant species for its nourishment. These crops were derived via several thousands of years of human selection that transformed wild ancestors into high-yielding domesticated descendants. Among cultivated plants, common bean (Phaseolus vulgaris L.) is the most important grain legume. Yet, our understanding of the origins and concurrent shaping of the genome of this crop plant is limited.[Results] We sequenced the genomes of 29 accessions representing 12 Phaseolus species. Single nucleotide polymorphism-based phylogenomic analyses, using both the nuclear and chloroplast genomes, allowed us to detect a speciation event, a finding further supported by metabolite profiling. In addition, we identified ~1200 protein coding genes (PCGs) and ~100 long non-coding RNAs with domestication-associated haplotypes. Finally, we describe asymmetric introgression events occurring among common bean subpopulations in Mesoamerica and across hemispheres.[Conclusions] We uncover an unpredicted speciation event in the tropical Andes that gave rise to a sibling species, formerly considered the “wild ancestor” of P. vulgaris, which diverged before the split of the Mesoamerican and Andean P. vulgaris gene pools. Further, we identify haplotypes strongly associated with genes underlying the emergence of domestication traits. Our findings also reveal the capacity of a predominantly autogamous plant to outcross and fix loci from different populations, even from distant species, which led to the acquisition by domesticated beans of adaptive traits from wild relatives. The occurrence of such adaptive introgressions should be exploited to accelerate breeding programs in the near future.This work was supported by the Ibero-American Programme for Science, Technology and Development - CYTED (PhasIbeAm project); Spanish Government - Ministry of Economy and Competitiveness (EUI2009-04052, BIO2011-26205), “Centro de Excelencia Severo Ochoa 2013-2017,” SEV-2012-0208 and Project PT13/0001/0021 (ISCIII - Subdirección General de Evaluación y Fomento de la Investigación/FEDER “Una Manera de hacer Europa”); Brazilian Government—National Council for Scientific and Technological Development - CNPq/Prosul (490725/2010-4); Ministerio de Ciencia, Tecnología e Innovación Productiva de la República Argentina; Consejo Nacional de Ciencia y Tecnología - Conacyt, Mexico (J010-214-2009, Fronteras 2015-2/814); and U.S. government: USDA National Institute of Food and Agriculture (2013-67013-21224. M. R-A. and J.M.M.-V. are indebted to Conacyt for a doctoral fellowship.Peer Reviewe

Global transcriptome analysis of the scorpion Centruroides noxius: new toxin families and evolutionary insights from an ancestral scorpion species.

Scorpion venoms have been studied for decades, leading to the identification of hundreds of different toxins with medical and pharmacological implications. However, little emphasis has been given to the description of these arthropods from cellular and evolutionary perspectives. In this report, we describe a transcriptomic analysis of the Mexican scorpion Centruroides noxius Hoffmann, performed with a pyrosequencing platform. Three independent sequencing experiments were carried out, each including three different cDNA libraries constructed from RNA extracted from the whole body of the scorpion after telson removal, and from the venom gland before and after venom extraction. Over three million reads were obtained and assembled in almost 19000 isogroups. Within the telson-specific sequences, 72 isogroups (0.4% of total unique transcripts) were found to be similar to toxins previously reported in other scorpion species, spiders and sea anemones. The annotation pipeline also revealed the presence of important elements of the small non-coding RNA processing machinery, as well as microRNA candidates. A phylogenomic analysis of concatenated essential genes evidenced differential evolution rates in this species, particularly in ribosomal proteins and proteasome components. Additionally, statistical comparison of transcript abundance before and after venom extraction showed that 3% and 2% of the assembled isogroups had higher expression levels in the active and replenishing gland, respectively. Thus, our sequencing and annotation strategies provide a general view of the cellular and molecular processes that take place in these arthropods, allowed the discovery of new pharmacological and biotechnological targets and uncovered several regulatory and metabolic responses behind the assembly of the scorpion venom. The results obtained in this report represent the first high-throughput study that thoroughly describes the universe of genes that are expressed in the scorpion Centruroides noxius Hoffmann, a highly relevant organism from medical and evolutionary perspectives