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

Genetic Relationships Among Peanut Cultivars and Breeding Lines in Shandong Province, PRC

Abstract Shandong province is the leading peanut-producing province in China which in turn is the leading peanut-producing country in the world. Shandong Peanut Research Institute (SPRI), an institute of the Shandong Academy of Agricultural Science, has had an ongoing breeding program for more than 40 yr and is the source of the peanut cultivars that dominate production in Shandong province and northern China. About 75 peanut cultivars and breeding lines have been released in Shandong by SPRI and other institutions. The genetic base of Shandong peanut cultivars has been described as narrow. The objective of this study was to (a) determine the genetic contribution of main ancestors to the genetic base of Shandong peanut cultivars and (b) study the genetic relationships among the peanut cultivars released in Shandong province during 1950-1999. Twentysix ancestors were identified in the pedigrees of 69 improved lines, 24 ancestors of Chinese origin contributed 96.1% of the Shandong peanut genetic base, and two exotic introductions contributed only 3.6%. The four most important ancestors based on average coancestry with the 69 improved lines are Fu Hua Sheng (PI 436545), Shi Tou Qi (PI 430227 and PI 461435), Jianggezhuang Ban Man (PI 433351), and Shuyang Da Zhan Yang from which 67, 28, 27 and 19 lines were derived, respectively. Among the 20 dominant cultivars of Shandong province, recently released cultivars Lu Hua 14 and Lu Hua 15 have the lowest average coancestry with the others which means those two new cultivars' have the high genetic divergence. In contrast, the very popular cultivars Fu Hua Sheng, Baisha 1016, Xuzhou 68-4, Lu Hua 9, and the new cultivar 8130 were closely related to the other cultivars. The results suggest that the genetic base of Shandong peanut cultivars released before 1990 is narrow, but that cultivars released after 1990 have broadened the genetic base due to introduction and use of new germplasm in the pedigrees. This information will be used as a guide for peanut breeders in choosing parents and avoiding genetic vulnerability to pests. For new cross combinations, parents with low coefficients of coancestry should be chosen in order to keep enlarging the gene pool of the new cultivars.</jats:p

Cultivar x Environment Interactions in Peanut Yield Tests1

Abstract Cultivar x environment interactions for yield and several fruit traits were estimated from two groups of Virginia peanut (Arachis hypogaea L.) cultivar yield trials conducted in the Virginia-North Carolina production area. A substantial cultivar x location x year second-order interaction was observed for yield in both studies. Both cultivar x location and cultivar x year interactions were small when compared to the variation among cultivars. No advantage could be gained by subdividing the production area into subareas for breeding or testing purposes. However, a reallocation of the number of plots presently used could give comparable estimates of cultivar performance and reduce the time necessary for cultivar evaluation.</jats:p