Nested‐association mapping (NAM)‐based genetic dissection uncovers candidate genes for seed and pod weights in peanut ( Arachis hypogaea )

Multiparental genetic mapping populations such as nested-association mapping (NAM) havegreat potential for investigating quantitative traits and associated genomic regions leading torapid discovery of candidate genes and markers. To demonstrate the utility and power of thisapproach, two NAM populations, NAM_Tifrunner and NAM_Florida-07, were used for dissectinggenetic control of 100-pod weight (PW) and 100-seed weight (SW) in peanut. Two high-densitySNP-based genetic maps were constructed with 3341 loci and 2668 loci for NAM_Tifrunner andNAM_Florida-07, respectively. The quantitative trait locus (QTL) analysis identified 12 and 8major effect QTLs for PW and SW, respectively, in NAM_Tifrunner, and 13 and 11 major effectQTLs for PW and SW, respectively, in NAM_Florida-07. Most of the QTLs associated with PW andSW were mapped on the chromosomes A05, A06, B05 and B06. A genomewide associationstudy (GWAS) analysis identified 19 and 28 highly significant SNP–trait associations (STAs) inNAM_Tifrunner and 11 and 17 STAs in NAM_Florida-07 for PW and SW, respectively. Thesesignificant STAs were co-localized, suggesting that PW and SW are co-regulated by severalcandidate genes identified on chromosomes A05, A06, B05, and B06. This study demonstratesthe utility of NAM population for genetic dissection of complex traits and performing high-resolution trait mapping in peanut

Reference genes for quantitative reverse transcription-polymerase chain reaction expression studies in wild and cultivated peanut

<p>Abstract</p> <p>Background</p> <p>Wild peanut species (<it>Arachis </it>spp.) are a rich source of new alleles for peanut improvement. Plant transcriptome analysis under specific experimental conditions helps the understanding of cellular processes related, for instance, to development, stress response, and crop yield. The validation of these studies has been generally accomplished by quantitative reverse transcription-polymerase chain reaction (qRT-PCR) which requires normalization of mRNA levels among samples. This can be achieved by comparing the expression ratio between a gene of interest and a reference gene which is constitutively expressed. Nowadays there is a lack of appropriate reference genes for both wild and cultivated <it>Arachis</it>. The identification of such genes would allow a consistent analysis of qRT-PCR data and speed up candidate gene validation in peanut.</p> <p>Results</p> <p>A set of ten reference genes were analyzed in four <it>Arachis </it>species (<it>A. magna</it>; <it>A. duranensis</it>; <it>A. stenosperma </it>and <it>A. hypogaea</it>) subjected to biotic (root-knot nematode and leaf spot fungus) and abiotic (drought) stresses, in two distinct plant organs (roots and leaves). By the use of three programs (GeNorm, NormFinder and BestKeeper) and taking into account the entire dataset, five of these ten genes, <it>ACT1 </it>(actin depolymerizing factor-like protein), <it>UBI1 </it>(polyubiquitin), <it>GAPDH </it>(glyceraldehyde-3-phosphate dehydrogenase), <it>60S </it>(60S ribosomal protein L10) and <it>UBI2 </it>(ubiquitin/ribosomal protein S27a) emerged as top reference genes, with their stability varying in eight subsets. The former three genes were the most stable across all species, organs and treatments studied.</p> <p>Conclusions</p> <p>This first in-depth study of reference genes validation in wild <it>Arachis </it>species will allow the use of specific combinations of secure and stable reference genes in qRT-PCR assays. The use of these appropriate references characterized here should improve the accuracy and reliability of gene expression analysis in both wild and cultivated Arachis and contribute for the better understanding of gene expression in, for instance, stress tolerance/resistance mechanisms in plants.</p

Genetic diversity of resident soil rhizobia isolated from nodules of distinct hairy vetch (\u3ci\u3eVicia villosa\u3c/i\u3e Roth) genotypes

Hairy vetch (Vicia villosa Roth, HV) is widely grown as a legume cover crop throughout the U.S.A., with biological nitrogen fixation (BNF) through symbiosis with Rhizobium leguminosarum biovar viciae (Rlv) being one of the most sought after benefits of its cultivation. This study determined if HV cultivation history and plant genotype affect genetic diversity of resident Rlv. Soil samples were collected from within farmers’ fields at Graham, Cedar Grove and Ivanhoe sites in North Carolina and pairs of genetically similar hairy vetch genotypes used as trap hosts. A total of 519 Rlv strains were isolated from six paired field soils, three with and three without histories of HV cultivation. A total of 46 strains failed to PCR-amplify the nifH gene; however nodC PCR amplification of these nifH-negative strains resulted in amplification of 22 of the strains. Repetitive element polymerase chain reaction (rep-PCR) with BOX-A1R primer and redundancy analysis showed rhizobial diversity to vary greatly within and between fields, with over 30 BOX banding patterns obtained across the six fields. Cluster analysis of BOX-PCR banding patterns resulted in 36 genetic groups of Rlv at a similarity level of 70%, with 15 of the isolates from fields with HV history not belonging to any of the clusters. Site was found to be the main driver of isolate diversity overall, explaining 57%, of the total variation among rhizobia occupying HV nodules, followed by history of hairy vetch cultivation. Evidence of a HV host genotype influence on the populations of rhizobia that infect hairy vetch was also observed, with plant genotype explaining 12.7% of the variation among all isolates. Our results show that second to site, HV cultivation history was the most important driver of rhizobial nodule community structure and increases the genetic diversity of resident Rlv in soils

Groundnut Breeding

Groundnut(Arachis hypogaea L.)are grown throughout the tropical and awarm tempearture regions of the world, with commercial production principally between latitudes 40 degree N and 40degree S. Leading production nations are India(33.4% of global production, China(27.8%), USA(9.3%), Senegal (4.2%), Indonesia (4.2%), Nigeria (3.3%), Myanmar(3.0%), Sudan(2.7%) and Argentina (2.0%). Clearly, the crop is grown in several agro ecological systems and under numerous socioeconomic environments. Yield of groundnuts is often…………………….

Effect of temperature on stability of components of resistance to cercospora arachidicola in peanut

Expression of resistance to early leaf spot disease of peanut, caused by Cercospora arachidicola, varies across diverse geographic locations. Environment is known to influence expression of partial resistance in some pathosystems and could affect stability of resistance to early leaf spot. Multiple components of resistance were studied at controlled temperatures on seven peanut genotypes selected at North Carolina State University and on six genotypes selected at ICRISAT in West Africa. The genotypes were inoculated with a North Carolina field isolate of C. arachidicola and incubated under day/night temperature regimes of 24/24, 26/20, 32/26, 38/26, and 38/32 C (the high-temperature regimes simulate the conditions in Niger, West Africa, and the cooler regimes simulate the conditions in North Carolina). Numbers of lesions were inversely related to temperature. Days after inoculation significantly influenced numbers of lesions and infection frequency. Regression of lesion numbers or infection frequencies on time and temperature accounted for 90% or more of experimental variation for 12 of 13 genotypes. Values for most resistance components examined (number of lesions, infection frequency, incubation period, lesion diameter, and necrotic area diameter) were dependent on both temperature and genotype. Several peanut genotypes were identified that expressed stable levels of resistance to C. arachidicola across temperature regimes. The North Carolina line 91 PA 150, derived from the wild diploid species Arachis cardenasii, consistently was ranked as resistant for all components in all temperature regimes. Other genotypes that ranked high in partial resistance to C. arachidicola included NC Ac 17894, PI 274194, NC Ac 18045, and 91 PA 131. Another group of genotypes, including GP-NC 343, NC 6, and N92069L, were moderately resistant. PI 476033 and NC 7 were highly susceptible at all temperatures, and N92064L varied in ranking for component