Inheritance of traits associated with seed size in groundnut (Arachis hypogaea L.)

Inheritance of groundnut (Arachis hypogaea L.) seed traits particularly seed weight, seed length, seed width and length:width ratio was explored in this study. Six-generation mean analysis was carried with two groundnut crosses and their reciprocals in 2 years. Groundnut genotypes significantly differing in seed sizes were used as parents. Highly significant reciprocal differences were observed for almost all the traits in F1, F2, and BC generations. Additive genetic effects were highly significant and explained majority of the variation in these traits. Results suggest that the seed size traits studied in this study were controlled both by combination of both maternal and nuclear gene effects. All the four seed traits measured were highly correlated suggesting that they could be simultaneously improved. Significance of additive effect in all the four crosses suggests that effective selection for seed size traits could be practiced in early generations. In breeding program for confectionary traits it is essential to include a large-seeded genotype as the female parent to exploit the maternal effects

Iron and zinc concentrations in peanut (Arachis hypogaea L.) seeds and their relationship with other nutritional and yield parameters

Biofortification (delivery of micronutrients via micronutrient-dense crops) can be achieved through plant breeding and offers a cost-effective and sustainable approach to fighting micronutrient malnutrition. The present study was conducted to facilitate the initiation of a breeding programme to improve the concentration of iron (Fe) and zinc (Zn) in peanut (Arachis hypogaea L.) seeds. The experiment was conducted with 64 diverse peanut genotypes for 2 years in eight different environments at the International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India to assess the genetic variation for Fe and Zn concentrations in peanut seeds and their heritability and correlations with other traits. Significant differences were observed among the genotypes and environments for Fe (33–68 mg/kg), Zn (44–95 mg/kg), protein (150–310 mg/g) and oil (410–610 mg/g) concentration in seeds and their heritability was high, thus indicating the possibility of improving them through breeding. As seen in other plants, a significant positive association between concentrations of Fe and Zn was observed. Trade-offs between pod yield and Fe and Zn concentrations were not observed and the same was also true for oil content. Besides being high yielding, genotypes ICGV 06099 (57 mg/kg Fe and 81 mg/kg Zn) and ICGV 06040 (56 mg/kg Fe and 80 mg/kg Zn) had stable performance for Fe and Zn concentrations across environments. These are the ideal choices for use as parents in a breeding programme and in developing mapping populations

Screening African rice (Oryza glaberrima) for tolerance to abiotic stresses: I. Fe toxicity

AbstractIron (Fe) toxicity is recognized as one of the most widely spread soil constraints for rice production especially in West Africa. Oryza glaberrima the cultivated rice species that originated from West Africa is well-adapted to its growing ecologies. The aim of this study was to identify the promising O. glaberrima accessions tolerant to Fe toxicity from the 2106 accessions held at the AfricaRice gene bank. The screenings were conducted over a four-year period and involved evaluating the entries under Fe-toxic field conditions in West Africa, selecting good yielding accessions and repeating the testing with newly selected lines. Three accessions (TOG 7206, TOG 6218-B and TOG 7250-A) were higher yielding than O. sativa checks under stress but with similar yields under control conditions. These accessions yielded over 300g/m2 under both Fe toxicity and control conditions. In conclusion, these materials could be used as donors in breeding programs for developing high yielding rice varieties suited to Fe toxicity affected areas in West Africa

Comparative transcriptome analysis of AP2/EREBP gene family under normal and hormone treatments, and under two drought stresses in NILs setup by Aday Selection and IR64

The AP2/EREBP genes play various roles in developmental processes and in stress-related responses in plants. Genome-wide microarrays based on the gene expression profiles of the AP2/EREBP family were analyzed under conditions of normal growth and drought stress. The preferential expression of fifteen genes was observed in specific tissues, suggesting that these genes may play important roles in vegetative and reproductive stages of growth. A large number of redundant genes were differentially expressed following phytohormone treatments (NAA, GA3, KT, SA, JA, and ABA). To investigate the gene expression responses in the root, leaf, and panicle of three rice genotypes, two drought stress conditions were applied using the fraction of transpirable soil water (FTSW) under severe (0.2 FTSW), mild (0.5 FTSW), and control (1.0 FTSW) conditions. Following treatment, transcriptomic analysis using a 44-K oligoarray from Agilent was performed on all the tissue samples. We identified common and specific genes in all tissues from two near-isogenic lines, IR77298-14-1-2-B-10 (drought tolerant) and IR77298-14-1-2-B-13 (drought susceptible), under drought stress conditions. The majority of the genes that were activated in the IR77298-14-1-2-B-10 line were members of the AP2/EREBP gene family. Non-redundant genes (sixteen) were found in the drought-tolerant line, and four genes were selected as candidate novel reference genes because of their higher expression levels in IR77298-14-1-2-B-10. Most of the genes in the AP2, B3, and B5 subgroups were involved in the panicle under severe stress conditions, but genes from the B1 and B2 subgroups were down-regulated in the root. Of the four subfamilies, RAV exhibited the highest number of up-regulated genes (80%) in the panicle under severe stress conditions in the drought-tolerant line compared to Minghui 63 under normal conditions, and the gene structures of the RAV subfamily may be involved in the response to drought stress in the flowering stage. These results provide a useful reference for the cloning of candidate genes from the specific subgroup for further functional analysis

Discovery of Pod Shatter-Resistant Associated SNPs by Deep Sequencing of a Representative Library Followed by Bulk Segregant Analysis in Rapeseed

Background: Single nucleotide polymorphisms (SNPs) are an important class of genetic marker for target gene mapping. As of yet, there is no rapid and effective method to identify SNPs linked with agronomic traits in rapeseed and other crop species. Methodology/Principal Findings: We demonstrate a novel method for identifying SNP markers in rapeseed by deep sequencing a representative library and performing bulk segregant analysis. With this method, SNPs associated with rapeseed pod shatter-resistance were discovered. Firstly, a reduced representation of the rapeseed genome was used. Genomic fragments ranging from 450–550 bp were prepared from the susceptible bulk (ten F2 plants with the silique shattering resistance index, SSRI,0.10) and the resistance bulk (ten F2 plants with SSRI.0.90), and also Solexa sequencingproduced 90 bp reads. Approximately 50 million of these sequence reads were assembled into contigs to a depth of 20-fold coverage. Secondly, 60,396 ‘simple SNPs ’ were identified, and the statistical significance was evaluated using Fisher’s exact test. There were 70 associated SNPs whose –log10p value over 16 were selected to be further analyzed. The distribution of these SNPs appeared a tight cluster, which consisted of 14 associated SNPs within a 396 kb region on chromosome A09. Our evidence indicates that this region contains a major quantitative trait locus (QTL). Finally, two associated SNPs from this region were mapped on a major QTL region

Germplasm Acquisition and Distribution by CGIAR Genebanks

The international collections of plant genetic resources for food and agriculture (PGRFA) hosted by 11 CGIAR Centers are important components of the United Nations Food and Agriculture Organization’s global system of conservation and use of PGRFA. They also play an important supportive role in realizing Target 2.5 of the Sustainable Development Goals. This paper analyzes CGIAR genebanks’ trends in acquiring and distributing PGRFA over the last 35 years, with a particular focus on the last decade. The paper highlights a number of factors influencing the Centers’ acquisition of new PGRFA to include in the international collections, including increased capacity to analyze gaps in those collections and precisely target new collecting missions, availability of financial resources, and the state of international and national access and benefit-sharing laws and phytosanitary regulations. Factors contributing to Centers’ distributions of PGRFA included the extent of accession-level information, users’ capacity to identify the materials they want, and policies. The genebanks’ rates of both acquisition and distribution increased over the last decade. The paper ends on a cautionary note concerning the potential of unresolved tensions regarding access and benefit sharing and digital genomic sequence information to undermine international cooperation to conserve and use PGRFA

Methylation matters: binding of Ets-1 to the demethylated Foxp3 gene contributes to the stabilization of Foxp3 expression in regulatory T cells

The forkhead-box protein P3 (Foxp3) is a key transcription factor for the development and suppressive activity of regulatory T cells (Tregs), a T cell subset critically involved in the maintenance of self-tolerance and prevention of over-shooting immune responses. However, the transcriptional regulation of Foxp3 expression remains incompletely understood. We have previously shown that epigenetic modifications in the CpG-rich Treg-specific demethylated region (TSDR) in the Foxp3 locus are associated with stable Foxp3 expression. We now demonstrate that the methylation state of the CpG motifs within the TSDR controls its transcriptional activity rather than a Treg-specific transcription factor network. By systematically mutating every CpG motif within the TSDR, we could identify four CpG motifs, which are critically determining the transcriptional activity of the TSDR and which serve as binding sites for essential transcription factors, such as CREB/ATF and NF-κB, which have previously been shown to bind to this element. The transcription factor Ets-1 was here identified as an additional molecular player that specifically binds to the TSDR in a demethylation-dependent manner in vitro. Disruption of the Ets-1 binding sites within the TSDR drastically reduced its transcriptional enhancer activity. In addition, we found Ets-1 bound to the demethylated TSDR in ex vivo isolated Tregs, but not to the methylated TSDR in conventional CD4+ T cells. We therefore propose that Ets-1 is part of a larger protein complex, which binds to the TSDR only in its demethylated state, thereby restricting stable Foxp3 expression to the Treg lineage

Differential Role for CD80 and CD86 in the Regulation of the Innate Immune Response in Murine Polymicrobial Sepsis

Inflammation in the early stages of sepsis is governed by the innate immune response. Costimulatory molecules are a receptor/ligand class of molecules capable of regulation of inflammation in innate immunity via macrophage/neutrophil contact. We recently described that CD80/86 ligation is required for maximal macrophage activation and CD80/86(-/-) mice display reduced mortality and inflammatory cytokine production after cecal ligation and puncture (CLP). However, these data also demonstrate differential regulation of CD80 and CD86 expression in sepsis, suggesting a divergent role for these receptors. Therefore, the goal of this study was to determine the individual contribution of CD80/86 family members in regulating inflammation in sepsis.CD80(-/-) mice had improved survival after CLP when compared to WT or CD86(-/-) mice. This was associated with preferential attenuation of inflammatory cytokine production in CD80(-/-) mice. Results were confirmed with pharmacologic blockade, with anti-CD80 mAb rescuing mice when administered before or after CLP. In vitro, activation of macrophages with neutrophil lipid rafts caused selective disassociation of IRAK-M, a negative regulator of NF-kappaB signaling from CD80; providing a mechanism for preferential regulation of cytokine production by CD80. Finally, in humans, upregulation of CD80 and loss of constitutive CD86 expression on monocytes was associated with higher severity of illness and inflammation confirming the findings in our mouse model.In conclusion, our data describe a differential role for CD80 and CD86 in regulation of inflammation in the innate immune response to sepsis. Future therapeutic strategies for blockade of the CD80/86 system in sepsis should focus on direct inhibition of CD80

Impact of the TCR Signal on Regulatory T Cell Homeostasis, Function, and Trafficking

Signaling through the T cell antigen receptor (TCR) is important for the homeostasis of naïve and memory CD4+ T cells. The significance of TCR signaling in regulatory T (Treg) cells has not been systematically addressed. Using an Ox40-cre allele that is prominently expressed in Treg cells, and a conditional null allele of the gene encoding p56Lck, we have examined the importance of TCR signaling in Treg cells. Inactivation of p56Lck resulted in abnormal Treg homeostasis characterized by impaired turnover, preferential redistribution to the lymph nodes, loss of suppressive function, and striking changes in gene expression. Abnormal Treg cell homeostasis and function did not reflect the involvement of p56Lck in CD4 function because these effects were not observed when CD4 expression was inactivated by Ox40-cre.The results make clear multiple aspects of Treg cell homeostasis and phenotype that are dependent on a sustained capacity to signal through the TCR