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Genome wide association studies (GWAS) can play an essential role in understanding genetic basis of complex traits in plants and animals. Conventional SNP-based linear mixed models (LMM) that marginally test single nucleotide polymorphisms (SNPs) have successfully identified many loci with major and minor effects in many GWAS. In plant, the relatively small population size in GWAS and the high genetic diversity found in many plant species can impede mapping efforts on complex traits. Here we present a novel haplotype-based trait fine-mapping framework, HapFM, to supplement current GWAS methods. HapFM uses genotype data to partition the genome into haplotype blocks, identifies haplotype clusters within each block, and then performs genome-wide haplotype fine-mapping to prioritize the candidate causal haplotype blocks of trait. We benchmarked HapFM, GEMMA, BSLMM, GMMAT, and BLINK in both simulated and real plant GWAS datasets. HapFM consistently resulted in higher mapping power than the other GWAS methods in high polygenicity simulation setting. Moreover, it resulted in smaller mapping intervals, especially in regions of high LD, achieved by prioritizing small candidate causal blocks in the larger haplotype blocks. In the Arabidopsis flowering time (FT10) datasets, HapFM identified four novel loci compared to GEMMA’s results, and the average mapping interval of HapFM was 9.6 times smaller than that of GEMMA. In conclusion, HapFM is tailored for plant GWAS to result in high mapping power on complex traits and improved on mapping resolution to facilitate crop improvement.

A molecular genetic characterization of the maize R-r complex of maize was completed during the period of support. The complex was shown to consist of two main regions: the P region, containing the r-p gene which controlled pigmentation of plant parts, and the S subcomplex, containing two rl-s genes in head-to-head orientation and a nonfunctional component termed rl-q. By examining the DNA sequences at the junction of the rl genes, the complex was shown to be derived by a series of abortive transposition events. The transposable element involved in the gene duplication and rearrangements was characterized and called doppia. Meiotic instability of the R-r complex was also characterized. Loss of P or S function was associated with several structural changes including intrachromosomal recombination and excision of a novel transposable element that appears to show instability only during meiosis.

This procedure is sometimes used with recalcitrant species or older plant tissues. Because the procedure employs a phenol:chloroform extraction it is slightly more time-consuming than the method described in the previous chapter and generates organic wastes. However, the recovered DNA usually digests well with restriction enzymes and stores for long periods without signs of degradation.

The original maize DNA miniprep protocol (version 1) and its successor, version 2, are used extensively for many plant species and different tissues. We (S.L. Dellaporta, J. Wood, J.B. Hicks) prefer this slightly modified version (2.1) for most large (ca. 50–100 µg) DNA extractions. This procedure has the advantage of speed, use of inexpensive reagents, and environmental soundness because neither phenol nor chloroform waste is generated.

Animals have evolved sophisticated immune systems to distinguish self from infectious non-self. In addition, several groups of colonial marine invertebrates—animals such as sponges, corals, and sea squirts—have evolved allorecognition systems that allow them to distinguish between their own tissues and those other members of their species. Allorecognition phenomena occur when these animals, which live as encrustations on marine surfaces, grow into contact with each other. Compatible colonies fuse, while incompatible colonies reject and often compete for space. Although allorecognition phenomena have long been known to be under genetic control, the molecular basis of these phenomena remains largely unknown. One model system for the study of invertebrate allorecognition is Hydractinia, a cnidarian related to Hydra and reef corals. Using lines of Hydractinia inbred for >8 generations, we have mapped allorecognition loci to a single genomic interval, called the allorecognition complex (ARC). The ARC contains at least two histocompatibility genes, alr1 and alr2, each of was identified by positional cloning. Both genes encode polymorphic transmembrane proteins similar to immunoglobulin superfamily (IgSF) molecules. Sequence variation between alleles of alr1 or alr2 is concentrated in the extracellular region and is predictive of allorecognition responses in inbred and wild-type colonies. Intriguingly, alr1 is located within a family of at least 10 other IgSF-like genes.