Daniel J. Fairbanks

Development, Characterization, and Linkage Mapping of Single Nucleotide Polymorphisms in the Grain Amaranths (Amaranthus sp.)

The grain amaranths (Amaranthus sp.) are important pseudo‐cereals native to the New World. During the last decade they have garnered increased international attention for their nutritional quality, tolerance to abiotic stress, and importance as a symbol of indigenous cultures. We describe the development of the first single nucleotide polymorphism (SNP) assays for amaranth. In addition, we report the characterization of the first complete genetic linkage map in the genus. The SNP assays are based on KASPar genotyping chemistry and were detected using the Fluidigm dynamic array platform. A diversity screen of 41 accessions of the cultivated amaranth species and their putative ancestor species (Amaranth hybridus L.) showed that the minor allele frequency (MAF) of these markers ranged from 0.05 to 0.5 with an average MAF of 0.27 per SNP locus. One hundred and forty‐one of the SNP loci were considered highly polymorphic (MAF ≥ 0.3). Linkage mapping placed all 411 markers into 16 linkage groups, presumably corresponding to each of the 16 amaranth haploid chromosomes. The map spans 1288 cM with an average marker density of 3.1 cM per marker. The work reported here represents the initial first steps toward the genetic dissection of agronomically important characteristics in amaranth.

Genetic relationship among 19 accessions of six species of Chenopodium L., by Random Amplified Polymorphic DNA fragments (RAPD)

The RAPD technique was used to identify genetic relationships in 19 accessions, including six species of the genus Chenopodium. A dendrogram was constructed using UPGMA from 399 DNA markers. The molecular data clustered species and accessions into five different groups. Group 1 with three cultivated varieties of C. nuttalliae, Group 2 included eight cultivars and two wild varieties of C. quinoa, Group 3 with C. berlandieri and C. album, Group 4 with two accessions of C. pallidicaule, and Group 5 with 2 accessions of C. ambrosioides. The polymorphic patterns generated by RAPD profiles showed different degrees of genetic relationship among the species studied. A low level of intraspecific variation was found within the accessions of C. quinoa, C. nuttalliae, and C. pallidicaule. The RAPD markers were found to be a useful tool for detecting genetic variation within the genus Chenopodium.

Mendelian controversies: a botanical and historical review

Gregor Mendel was a 19(th) century priest and botanist who developed the fundamental laws of inheritance. The year 2000 marked a century since the rediscovery of those laws and the beginning of genetics. Although Mendel is now recognized as the founder of genetics, significant controversy ensued about his work throughout the 20(th) century. In this paper, we review five of the most contentious issues by looking at the historical record through the lens of current botanical science: (1) Are Mendels data too good to be true? (2) Is Mendels description of his experiments fictitious? (3) Did Mendel articulate the laws of inheritance attributed to him? (4) Did Mendel detect but not mention linkage? (5) Did Mendel support or oppose Darwin?A synthesis of botanical and historical evidence supports our conclusions: Mendel did not fabricate his data, his description of his experiments is literal, he articulated the laws of inheritance attributed to him insofar as was possible given the information he had, he did not detect linkage, and he neither strongly supported nor opposed Darwin.

Male-specific DNA in the dioecious species Atriplex garrettii (Chenopodiaceae).

The mechanism of sex determination in dioecious species of the genus Atriplex (Chenopodiaceae) has not been determined. This paper reports the discovery of a male-specific DNA fragment in the diploid dioecious species A. garrettii. DNA samples extracted individually from ten male and ten female plants were bulked by sex. Random amplified polymorphic DNA (RAPD) fragments were generated in the two bulks in order to identify markers that were polymorphic between male and female plants. A total of 158 decamer primers were tested. A 2075 base-pair (bp) male-specific DNA fragment generated with the OPAF-14 primer was identified. The fragment was cloned and partially sequenced and 24-mer primers that exclusively amplified this fragment were constructed. When 124 male plants, 126 female plants, and one hermaphroditic plant were tested individually, the male-specific 2075-bp DNA fragment was present in the hermaphrodite and all but one of the male plants, and was absent in all female plants. A smaller DNA fragment (~1800 bp) that was homologous to the 2075-bp fragment was amplified from the single male plant that lacked the 2075-bp fragment. Cytogenetic analysis revealed no apparent heteromorphic sex chromosomes. These observations suggest that sex determination in A. garrettii is genetic, with no evidence of heteromorphic sex chromosomes.

Correlation between molecular markers and adaptively significant genetic variation in Bromus tectorum (Poaceae), an inbreedingannual grass

Single sequence repeat (SSR) and amplified fragment length polymorphic (AFLP) molecular marker genotypes in cheatgrass (Bromus tectorum) were compared to published data on phenotypic variation in seed dormancy, vernalization requirement, and resistance to the pathogen Ustilago bullata. Several features of cheatgrass facilitated this study: it is a recent invader in the western United States, has considerable phenotypic polymorphism, and is an obligate self-pollinator. Forty self-pollinating lines from four populations common to the three phenotypic data sets were analyzed for molecular genetic variation using seven SSR loci and 31 AFLP loci. We examined correlations between distance matrices using the Mantel test for each pair of studies. The two molecular data sets were significantly correlated (r = 0.636). The AFLP markers often distinguished among several lines with identical SSR genotypes. The AFLP data were also significantly correlated with the phenotypic data (r values from 0.4640 to 0.5658), but the SSR data were much more highly correlated (r values from 0.677 to 0.844). The difference between molecular marker systems was especially notable when an outlier population from Potosi Pass, Nevada, was excluded from the analysis. These results suggest that SSR markers may be good surrogates for phenotypic traits in population genetic studies of strongly inbreeding species such as cheatgrass.

Root iron‐reduction capacity for genotypic evaluation of iron efficiency in soybean

Abstract Genetic resistance to Fe‐deficiency chlorosis is the most viable and economical means to overcome this problem in soybean [Glycine max (L.) Merr.], but current field evaluation is slowed and constrained by soil heterogeneity and environmental fluctuation. Highly resistant (Fe‐efficient) cultivars have been shown to reduce Fe3+ to Fe2+ more actively by the roots under Fe‐deficiency stress than highly susceptible genotypes. The objective of this study was to determine if Fe3+ reduction could be used to predict the degree of resistance or susceptibility to Fe‐deficiency chlorosis. Thirteen genotypes (both commercial and experimental) with known field susceptibility ratings were grown in a growth chamber in modified Hoagland solution. The more Fe‐efficient genotypes reduced Fe3+ earlier and to a greater extent than the less Fe‐efficient types. The sum of the seven daily Fe3+ reduction measurements was negatively correlated with field chlorosis ratings, as high as ‐0.864 (p > 0.01), and was a good pre...

Evolution of the NANOG pseudogene family in the human and chimpanzee genomes

BackgroundThe NANOG gene is expressed in mammalian embryonic stem cells where it maintains cellular pluripotency. An unusually large family of pseudogenes arose from it with one unprocessed and ten processed pseudogenes in the human genome. This article compares the NANOG gene and its pseudogenes in the human and chimpanzee genomes and derives an evolutionary history of this pseudogene family.ResultsThe NANOG gene and all pseudogenes except NANOGP8 are present at their expected orthologous chromosomal positions in the chimpanzee genome when compared to the human genome, indicating that their origins predate the human-chimpanzee divergence. Analysis of flanking DNA sequences demonstrates that NANOGP8 is absent from the chimpanzee genome.ConclusionBased on the most parsimonious ordering of inferred source-gene mutations, the deduced evolutionary origins for the NANOG pseudogene family in the human and chimpanzee genomes, in order of most ancient to most recent, are NANOGP6, NANOGP5, NANOGP3, NANOGP10, NANOGP2, NANOGP9, NANOGP7, NANOGP1, and NANOGP4. All of these pseudogenes were fixed in the genome of the human-chimpanzee common ancestor. NANOGP8 is the most recent pseudogene and it originated exclusively in the human lineage after the human-chimpanzee divergence. NANOGP1 is apparently an unprocessed pseudogene. Comparison of its sequence to the functional NANOG genes reading frame suggests that this apparent pseudogene remained functional after duplication and, therefore, was subject to selection-driven conservation of its reading frame, and that it may retain some functionality or that its loss of function may be evolutionarily recent.

Assessment of genetic diversity in the USDA and CIP-FAO international nursery collections of quinoa (Chenopodium quinoa Willd.) using microsatellite markers

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 Ballon. Using the patterns of genetic diversity detected within the C. quinoa accessions we discuss hypotheses regarding quinoas 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.

Simple sequence repeat marker development and genetic mapping in quinoa (Chenopodium quinoa Willd.)

Quinoa is a regionally important grain crop in the Andean region of South America. Recently quinoa has gained international attention for its high nutritional value and tolerances of extreme abiotic stresses. DNA markers and linkage maps are important tools for germplasm conservation and crop improvement programmes. Here we report the development of 216 new polymorphic SSR (simple sequence repeats) markers from libraries enriched for GA, CAA and AAT repeats, as well as 6 SSR markers developed from bacterial artificial chromosome-end sequences (BES-SSRs). Heterozygosity (H) values of the SSR markers ranges from 0.12 to 0.90, with an average value of 0.57. A linkage map was constructed for a newly developed recombinant inbred lines (RIL) population using these SSR markers. Additional markers, including amplified fragment length polymorphisms (AFLPs), two 11S seed storage protein loci, and the nucleolar organizing region (NOR), were also placed on the linkage map. The linkage map presented here is the first SSR-based map in quinoa and contains 275 markers, including 200 SSR. The map consists of 38 linkage groups (LGs) covering 913 cM. Segregation distortion was observed in the mapping population for several marker loci, indicating possible chromosomal regions associated with selection or gametophytic lethality. As this map is based primarily on simple and easily-transferable SSR markers, it will be particularly valuable for research in laboratories in Andean regions of South America.

Isolation and characterization of atriplex hortensis and sweet chenopodium quinoa starches

ABSTRACT Starches from garden orach (Atriplex hortensis) and sweet quinoa (Chenopodium quinoa Willd. ‘Surumi’) seeds were isolated, examined for compositional characteristics, and compared with bitter quinoa (Cheno-podium quinoa Willd.) starch. Garden orach and sweet quinoa seeds were similar in fat and ash contents, while garden orach seeds contained ≈10% more protein. Starches were isolated from seeds following a 12-hr soak in dilute alkaline solution using a series of grinding, screening, centrifugation, and washing steps. Isolated starches viewed by scanning electron microscopy yielded angular, polygonal granules ≈1–2 μm in diameter. Starches displayed typical A-type crystalline packing arrangements as determined by X-ray powder diffractometry. Apparent amylose contents for garden orach (21.2%), sweet quinoa (20.6%), and bitter quinoa (19.8%) were determined according to colorimetric procedure. Differential scanning calorimetry data indicated a higher and wider gelatinization temperature range for gar...