Browsing by Autor "Daniel J. Fairbanks"

Now showing 1 - 10 of 10

A genetic linkage map of quinoa (Chenopodium quinoa) based on AFLP, RAPD, and SSR markers
(Springer Science+Business Media, 2004) Peter J. Maughan; Alejandro Bonifacio; Eric N. Jellen; Mikel R. Stevens; Craig E. Coleman; M.L. Ricks; Sara Mason; David E. Jarvis; Brian Gardunia; Daniel J. Fairbanks
Assessment of genetic diversity in the USDA and CIP-FAO international nursery collections of quinoa (Chenopodium quinoa Willd.) using microsatellite markers
(Cambridge University Press, 2007) Shawn A. Christensen; Donald B. Pratt; Charles S. Pratt; Paul Nelson; Mikel R. Stevens; Eric N. Jellen; Craig E. Coleman; Daniel J. Fairbanks; Alejandro Bonifacio; Peter J. Maughan
Quinoa ( Chenopodium quinoa Willd.) is a staple food crop for millions of impoverished rural inhabitants of Andean South America where it has been cultivated for millennia. Interest in quinoa, due largely to its superior nutritional characteristics, is fuelling a growing export market and has led to an increased focus on genetic research and the development of quinoa breeding programmes throughout South America. The success of these breeding programmes will rely heavily on the development of core germplasm collections and germplasm conservation. We report the development of a set of fluorescence-tagged microsatellite molecular markers that can be used to characterize genetic diversity within quinoa germplasm and we use this set of 36 microsatellites markers to genetically characterize the diversity of 121 accessions of C. quinoa held in the USDA germplasm bank, 22 accessions from the CIP-FAO international nursery collection and eight accessions representing parents from genetic mapping populations. A total of 420 alleles were detected among the quinoa accessions with an average of 11 alleles detected per microsatellite locus. Genetic heterogeneity was observed in 32% of the quinoa accessions at a given locus and suggests that many of these accessions represent heterogeneous seed lots or landraces. Both unweighted pair-group method with arithmetic averages (UPGMA) and principle components analysis (PCA) analyses partitioned the quinoa accessions into two main clusters. The first major cluster consisted of accessions from the Andean highlands of Peru, Bolivia, Ecuador, Argentina and extreme northeastern Chile. The other main cluster contained accessions from both the lowlands of Chile and a set of USDA accessions with no known passport data, collected by Emigdio Ballón. Using the patterns of genetic diversity detected within the C. quinoa accessions we discuss hypotheses regarding quinoa's centre of diversity, including highland and lowland ecotype clustering patterns, origin of lowland varieties, origin of domestication, and diversity levels in the USDA and CIP-FAO collections.
Characterization of Salt Overly Sensitive 1 (SOS1) gene homoeologs in quinoa (Chenopodium quinoa Willd.)
(NRC Research Press, 2009) Peter J. Maughan; T.B. Turner; Craig E. Coleman; D. B. Elzinga; Eric N. Jellen; Jorge Morales; Joshua A. Udall; Daniel J. Fairbanks; Alejandro Bonifacio
Salt tolerance is an agronomically important trait that affects plant species around the globe. The Salt Overly Sensitive 1 (SOS1) gene encodes a plasma membrane Na+/H+ antiporter that plays an important role in germination and growth of plants in saline environments. Quinoa (Chenopodium quinoa Willd.) is a halophytic, allotetraploid grain crop of the family Amaranthaceae with impressive nutritional content and an increasing worldwide market. Many quinoa varieties have considerable salt tolerance, and research suggests quinoa may utilize novel mechanisms to confer salt tolerance. Here we report the cloning and characterization of two homoeologous SOS1 loci (cqSOS1A and cqSOS1B) from C. quinoa, including full-length cDNA sequences, genomic sequences, relative expression levels, fluorescent in situ hybridization (FISH) analysis, and a phylogenetic analysis of SOS1 genes from 13 plant taxa. The cqSOS1A and cqSOS1B genes each span 23 exons spread over 3477 bp and 3486 bp of coding sequence, respectively. These sequences share a high level of similarity with SOS1 homologs of other species and contain two conserved domains, a Nhap cation-antiporter domain and a cyclic-nucleotide binding domain. Genomic sequence analysis of two BAC clones (98 357 bp and 132 770 bp) containing the homoeologous SOS1 genes suggests possible conservation of synteny across the C. quinoa sub-genomes. This report represents the first molecular characterization of salt-tolerance genes in a halophytic species in the Amaranthaceae as well as the first comparative analysis of coding and non-coding DNA sequences of the two homoeologous genomes of C. quinoa.
Construction of a quinoa (Chenopodium quinoa Willd.) BAC library and its use in identifying genes encoding seed storage proteins
(Springer Science+Business Media, 2006) Mikel R. Stevens; Craig E. Coleman; Susan E. Parkinson; Peter J. Maughan; H.-B. Zhang; Marie Balzotti; David L. Kooyman; K. Arumuganathan; Alejandro Bonifacio; Daniel J. Fairbanks
Development and use of an expressed sequenced tag library in quinoa (Chenopodium quinoa Willd.) for the discovery of single nucleotide polymorphisms
(Elsevier BV, 2004) Nathan D. Coles; Craig E. Coleman; Shawn A. Christensen; Eric N. Jellen; Mikel R. Stevens; Alejandro Bonifacio; J. Rojas‐Beltrán; Daniel J. Fairbanks; Peter J. Maughan
Development and Use of Microsatellite Markers for Germplasm Characterization in Quinoa (Chenopodium quinoa Willd.)
(Wiley, 2005) Sara Mason; Mikel R. Stevens; Eric N. Jellen; Alejandro Bonifacio; Daniel J. Fairbanks; Craig E. Coleman; Ronald McCarty; Andrew Rasmussen; Peter J. Maughan
Quinoa ( Chenopodium quinoa Willd.) is a widely consumed food crop and a primary protein source for many of the indigenous inhabitants of the Andean region of South America. The objective of this study was to develop a collection of reproducible and highly informative microsatellite markers for quinoa. A total of 1276 clones were sequenced from three microsatellite‐enriched (CA, ATT, ATG) libraries. Four hundred fifty‐seven (36%) of the clones contained unique microsatellites. The most common repeated motifs, other than CA, AAT, and ATG, were GA and CAA. Flanking primers were designed for 397 microsatellite loci and screened using a panel of diverse quinoa accessions and one accession of C. berlandieri Moq., a wild relative of quinoa. Two hundred eight (52%) of the microsatellite markers were polymorphic among the quinoa accessions. An additional 25 of the microsatellite markers (6%) were polymorphic when the C. berlandieri accession was included in the analysis. Only in rare instances (nine) did a microsatellite amplify in quinoa and not in C. berlandieri The number of observed alleles ranged from 2 to 13, with an average of four alleles detected per locus. Heterozygosity values ranged from 0.20 to 0.90 with a mean value of 0.57. Sixty‐seven markers (32%) were highly polymorphic ( H ≥ 0.70). These microsatellites markers are an ideal resource for use in managing quinoa germplasm, trait mapping and marker‐assisted breeding strategies. The wide cross‐species transportability of these markers may extend their value to research involving other Chenopodium species.
Genetic relationship among 19 accessions of six species of Chenopodium L., by Random Amplified Polymorphic DNA fragments (RAPD)
(Springer Science+Business Media, 1999) Paulo Maurício Ruas; Paulo Maurício Ruas; Paulo Maurício Ruas; Alejandro Bonifacio; Alejandro Bonifacio; Claudete F. Ruas; Claudete F. Ruas; Daniel J. Fairbanks
Quinoa (Chenopodium quinoa)
(2007) Peter J. Maughan; Alejandro Bonifacio; Craig E. Coleman; Eric N. Jellen; Mikel R. Stevens; Daniel J. Fairbanks
Simple sequence repeat marker development and genetic mapping in quinoa (Chenopodium quinoa Willd.)
(Springer Nature, 2008) David E. Jarvis; Olga R. Kopp; Eric N. Jellen; Melanie A. Mallory; Jack Pattee; Alejandro Bonifacio; Craig E. Coleman; Mikel R. Stevens; Daniel J. Fairbanks; Peter J. Maughan
Single Nucleotide Polymorphism Identification, Characterization, and Linkage Mapping in Quinoa
(Crop Science Society of America, 2012) Peter J. Maughan; Scott M. Smith; J. Rojas‐Beltrán; D. B. Elzinga; Joshua A. Raney; Eric N. Jellen; Alejandro Bonifacio; Joshua A. Udall; Daniel J. Fairbanks
Quinoa ( Chenopodium quinoa Willd.) is an important seed crop throughout the Andean region of South America. It is important as a regional food security crop for millions of impoverished rural inhabitants of the Andean Altiplano (high plains). Efforts to improve the crop have led to an increased focus on genetic research. We report the identification of 14,178 putative single nucleotide polymorphisms (SNPs) using a genomic reduction protocol as well as the development of 511 functional SNP assays. The SNP assays are based on KASPar genotyping chemistry and were detected using the Fluidigm dynamic array platform. A diversity screen of 113 quinoa accessions showed that the minor allele frequency (MAF) of the SNPs ranged from 0.02 to 0.50, with an average MAF of 0.28. Structure analysis of the quinoa diversity panel uncovered the two major subgroups corresponding to the Andean and coastal quinoa ecotypes. Linkage mapping of the SNPs in two recombinant inbred line populations produced an integrated linkage map consisting of 29 linkage groups with 20 large linkage groups, spanning 1404 cM with a marker density of 3.1 cM per SNP marker. The SNPs identified here represent important genomic tools needed in emerging plant breeding programs for advanced genetic analysis of agronomic traits in quinoa.