LEARNING The objectives of BIOS 781 are to present: OBJECTIVES: 1. basic population and quantitative genetic principles, including classical genetics, chromosomal theory of inheritance, and meiotic recombination 2. an exposure to QTL mapping methods of complex quantitative traits and linkage methods to detect co-segregation with disease 3. methods for assessing marker-disease linkage disequilibrium, including case-control approaches 4. methods for genome-wide association and stratification control.

Genetic Data Analysis

We constructed a genetic linkage map for a tetraploid derivative species, the rainbow trout (Oncorhynchus mykiss), using 191 microsatellite, 3 RAPD, 7 ESMP, and 7 allozyme markers in three backcross families. The linkage map consists of 29 linkage groups with potential arm displacements in the female map due to male-specific pseudolinkage arrangements. Synteny of duplicated microsatellite markers was used to identify and confirm some previously reported pseudolinkage arrangements based upon allozyme markers. Fifteen centromeric regions (20 chromosome arms) were identified with a half-tetrad analysis using gynogenetic diploids. Female map length is approximately 10 M, but this is a large underestimate as many genotyped segments remain unassigned at a LOD threshold of 3.0. Extreme differences in female:male map distances were observed (ratio F:M, 3.25:1). Females had much lower recombination rates (0.14:1) in telomeric regions than males, while recombination rates were much higher in females within regions proximal to the centromere (F:M, 10:1). Quadrivalent formations that appear almost exclusively in males are postulated to account for the observed differences.

https://www.genetics.org/content/genetics/155/3/1331.full.pdf

A Microsatellite Linkage Map of Rainbow Trout (Oncorhynchus mykiss) Characterized by Large Sex-Specific Differences in Recombination Rates

Afforestation, the conversion of non-forested lands to forest plantations, can sequester atmospheric carbon dioxide, but the rapid growth and harvesting of biomass may deplete nutrients and degrade soils if managed improperly. The goal of this study is to evaluate how afforestation affects mineral soil quality, including pH, sodium, exchangeable cations, organic carbon, and nitrogen, and to examine the magnitude of these changes regionally where afforestation rates are high. We also examine potential mechanisms to reduce the impacts of afforestation on soils and to maintain long-term productivity. Across diverse plantation types (153 sites) to a depth of 30 cm of mineral soil, we observed significant decreases in nutrient cations (Ca, K, Mg), increases in sodium (Na), or both with afforestation. Across the data set, afforestation reduced soil concentrations of the macronutrient Ca by 29% on average (P , 0.05). Afforestation by Pinus alone decreased soil K by 23% (P , 0.05). Overall, plantations of all genera also led to a mean 71% increase of soil Na (P , 0.05). Mean pH decreased 0.3 units (P , 0.05) with afforestation. Afforestation caused a 6.7% and 15% (P , 0.05) decrease in soil C and N content respectively, though the effect was driven principally by Pinus plantations (15% and 20% decrease, P , 0.05). Carbon to nitrogen ratios in soils under plantations were 5.7-11.6% higher (P , 0.05). In several regions with high rates of afforestation, cumulative losses of N, Ca, and Mg are likely in the range of tens of millions of metric tons. The decreases indicate that trees take up considerable amounts of nutrients from soils; harvesting this biomass repeatedly could impair long-term soil fertility and productivity in some locations. Based on this study and a review of other literature, we suggest that proper site preparation and sustainable harvest practices, such as avoiding the removal or burning of harvest residue, could minimize the impact of afforestation on soils. These sustainable practices would in turn slow soil compaction, erosion, and organic matter loss, maintaining soil fertility to the greatest extent possible.

/pdf/a-global-meta-analysis-of-soil-exchangeable-cations-ph-4jtmtopit9.pdf

A global meta-analysis of soil exchangeable cations, pH, carbon, and nitrogen with afforestation.

An amplified fragment polymorphism (AFLP) based linkage map has been generated for a new Landsberg erecta/ Cape Verde Islands (Ler/Cvi) recombinant inbred line (RIL) population. A total of 321 molecular PCR based markers and the erecta mutation were mapped. AFLP markers were also analysed in the Landsberg erecta/Columbia (Ler/Col) RIL population (Lister and Dean, 1993) and 395 AFLP markers have been integrated into the previous Arabidopsis molecular map of 122 RFLPs, CAPSs and SSLPs. This enabled the evaluation of the efficiency and robustness of AFLP technology for linkage analyses in Arabidopsis. AFLP markers were found throughout the linkage map. The two RIL maps could be integrated through 49 common markers which all mapped at similar positions. Comparison of both maps led to the conclusion that segregating bands from a common parent can be compared between different populations, and that AFLP bands of similar molecular size, amplified with the same primer combination in two different ecotypes, are likely to correspond to the same locus. AFLPs were found clustering around the centromeric regions, and the authors have established the map position of the centromere of chromosome 3 by a quantitative analysis of AFLP bands using trisomic plants. AFLP markers were also used to estimate the polymorphism rate among the three ecotypes. The larger polymorphism rate found between Ler and Cvi compared to Ler and Col will mean that the new RIL population will provide a useful material to map DNA polymorphisms and quantitative trait loci.

Development of an AFLP based linkage map of Ler, Col and Cvi Arabidopsis thaliana ecotypes and construction of a Ler/Cvi recombinant inbred line population

Recent advances in molecular technology have opened a new chapter in species conservation efforts, as well as population biology. DNA sequencing, MHC (major histocompatibility complex), minisatellite, microsatellite, and RAPD (random amplified polymorphic DNA) procedures allow for identification of parentage, more distant relatives, founders to new populations, unidentified individuals, population structure, effective pop- ulation size, population-specific markers, etc. PCR (polymerase chain reaction) amplifi- cation of mitochondrial DNA, nuclear DNA, ribosomal DNA, chloroplast DNA, and other systems provide for more sophisticated analyses of metapopulation structure, hybridization events, and delineation of species, subspecies, and races, all of which aid in setting species recovery priorities. Each technique can be powerful in its own right but is most credible when used in conjunction with other molecular techniques and, most importantly, with ecological and demographic data collected from the field. Surprisingly few taxa of concern have been assayed with any molecular technique. Thus, rather than showcasing exhaustive details from a few well-known examples, this paper attempts to present a broad range of cases in which molecular techniques have been used to provide insight into conservation efforts.

https://www.jstor.org/stable/pdfplus/176942.pdf

Molecular contributions to conservation

Genetic marker systems have improved dramatically in the past 10 yr. Each new system needs to be evaluated for its distribution of markers on genetic linkage maps to validate its use for genetic analysis. The resulting maps are also useful for establishing the genetic positions of genes affecting important phenotypes. We have constructed a high density map in soybean [Glycine max (L.) Merr.] using a 300 RIL (recombinant inbred line) population from BSR-101 x PI437.654 by first constructing an RFLP (restriction fragment length polymorphism) scaffold map based on the entire population. The RFLP anchored map was then further populated with AFLP (amplified fragment length polymorphism) markers based on only a 42 RIL subset. We report here an 840 marker map consisting of 165 RFLP, 25 RAPD (random amplified polymorphic DNA), and 650 AFLP markers spread over 28 linkage groups representing 3441 cM distance. Although clustering of AFLP markers occurred, markers were mapped to every linkage group and were well distributed relative to other marker systems. The AFLP marker system appears to be a useful approach for generating high density genetic maps in soybean.

A High-Density Soybean Genetic Map Based on AFLP Markers

Timber investment returns were estimated for the principal exotic and selected native species in the Southern Cone of Latin America and in the Southern United States. Exotic eucalyptus plantations in South America were most profitable, with internal rates of returns (IRRs) ranging from 13% to 23%, followed by exotic loblolly pine, with IRRs from 9% to 17%. Average loblolly pine plantation returns in the US South were less profitable, with an IRR of about 9.5%, and natural forest management in the South had IRRs of 4% to 8%. Subtropical native species plantations of the best araucaria and nothofagus species had reasonable financial returns, with IRRs ranging from 5% to 13%. Subtropical or tropical native forests had fewer commercial timber species, and had much lower growth rates and returns. Their IRRs were less than 4%, or even negative for unmanaged stands. State subsidy payments for forest plantations or for timber stand improvements increased IRRs somewhat and reserving areas for environmental protection reduced their IRRs slightly. Including land costs in the cash flows decreased these internal rates of return substantially. Natural stand returns in Latin America were much less than those of plantations, but management of those stands offered better rates of return than only holding the land.

Timber investment returns for selected plantations and native forests in South America and the Southern United States

Amphibians in the south-western United States are currently experiencing population declines. Causal explanations for these population changes as well as the implementation of sound management practices requires an understanding of the genetic structure of natural amphibian populations. To this end, we estimated genetic differences within and among seven isolated populations of northern leopard frogs, Rana pipiens, from Arizona and southern Utah using random amplified polymorphic DNA (RAPD) analyses. Fourteen arbitrarily designed primers detected 38 polymorphic loci in 85 individual frogs. Three types of population structure were observed in this study. (i) Two populations showed low genetic diversity (D = 0.10 and 0.04) and may have been established by relatively recent events. (ii) Two were not genetically distinct and exhibited a high degree of within-population diversity (D = 0.35). The possibility of gene flow between these populations is high due to their geographical proximity and their shared genetic structure. (iii) Three populations were genetically distinct from each other and the other populations, and exhibited intermediate within-population variation (D = 0.19, 0.17, 0.14). Genetic distances among the seven populations ranged from 0.00 to 0.20, suggesting that some of these leopard frog populations are genetically distinct. Although based on relatively small samples, these data suggest that leopard frog populations in the south-west are likely to represent unique genetic entities worthy of conservation. The management implications of these results are that isolated leopard frog populations should be evaluated on an individual basis to best preserve them.

RAPD marker estimation of genetic structure among isolated northern leopard frog populations in the south-western USA

A 356-marker linkage map of Glycine max (L.) Merr. (2n = 20) was established by anchoring 106 RAPD markers to an existing RFLP map built with a large recombinant inbred line population (330 RILs). This map comprises 24 major and 11 minor linkage groups for this genome which is estimated to be approximately 3,275 cM. The RAPD markers show similar distribution throughout the genome and identified similar levels of polymorphism as the RFLP markers used in the framework. By using a subset population to anchor the RAPD markers, it was possible to enhance the throughput of selecting and adding reliable marker loci to the existing map. The procedures to generate a dependable genetic linkage map are also described in this report.

Soybean genetic map of RAPD markers assigned to an existing scaffold RFLP map

Random amplified polymorphic DNA (RAPD) is based on DNA amplification by polymerase chain reaction (PCR) of random DNA segments using single arbitrary nucleotide sequences. We have adapted the assay to soybeans by using Stoffel Fragment DNA polymerase and by optimizing the reaction conditions. To increase the percentage of RAPD polymorphisms, the DNA template was digested with restriction enzymes before amplification. The combination of twenty-four primers and five DNA template treatments (Undigested, DraI, EcoRI, HindIII, and TaqI digested) revealed 94 polymorphic DNA fragments differing between soybean lines PI437654 and BSR101. Many polymorphic DNA bands were found unreliable or non-scoreable after re-screening of primers and verification of marker-allele segregation with 20 recombinant inbred lines (RILs). However, 28 RAPD markers were consistently polymorphic between the parental lines and followed Mendelian expectations. The use of DNA templates digested with DraI, EcoRI, HindIII or TaqI increased three times the number of RAPD markers compared to undigested DNA template alone. The 28 RAPD markers obtained were further screened with 72 RILs and placed on an existing RFLP map.

Arnaldo Ribeiro Ferreira

Papers

A High-Density Soybean Genetic Map Based on AFLP Markers

Timber investment returns for selected plantations and native forests in South America and the Southern United States

RAPD marker estimation of genetic structure among isolated northern leopard frog populations in the south-western USA

Soybean genetic map of RAPD markers assigned to an existing scaffold RFLP map

Genetic Mapping of Soybean (Glycine max (L.) Merr.) Using Random Amplified Polymorphic DNA (RAPD)