Identification of Cis-Regulatory Modules that Function in the Male Germline of Flowering Plants.

The male germline of flowering plants develops within the vegetative cell of the male gametophyte and displays a distinct transcriptional profile. Key to understanding the development of this unique cell lineage is determining how gene expression is regulated within germline cells. This knowledge impacts upon our understanding of cell specification, differentiation, and plant fertility. Here, we describe methods to identify cis-regulatory modules (CRMs) that act as key regulatory regions in the promoters of germline-expressed genes. We detail the complimentary techniques of phylogenetic footprinting and the use of fluorescent reporters in pollen for the identification and verification of CRMs

Additional file 1: Table S1. of Lack of direct evidence for natural selection at the candidate thrifty gene locus, PPARGC1A

Fourteen previously detected combinations of populations and genes from Voight et al. (2006) were analysed using the selscan software package (Szpiech and Hernandez 2014) as positive controls to provide insight into possible power of detection of signatures of selection. Seven of the previously detected 14 associations were repeated, where we defined evidence of selection as >1 SNP exceeding the 5% threshold of iHS values. For two genes (LCT in both CEU and GBR populations and SLC44A5 in CHS and CHB populations) showed evidence of selection in populations with similar ancestry (Caucasian and Asian, respectively). Evidence of selection for one other gene (SNTG1) was observed in only one of two populations with the same ethnicity. (DOCX 25 kb

Additional file 3: Figures S2a-c. of Lack of direct evidence for natural selection at the candidate thrifty gene locus, PPARGC1A

Fay and Wu’s H calculated across chromosome 4 using a 30 kbp sliding window. Chromosome 4:22.7–24.9 Mbp is shown with chromosome mean (blue) and 2.5%, 97.5% quantiles (purple) from Table 4 marked. Location of PPARGC1A is marked in red. Rs8192678 is marked by a red dashed line. Figure S2b Fay and Wu’s H calculated across chromosome 4 using a 5 kbp sliding window. Chromosome 4:22.7–24.9 Mbp is shown with chromosome mean (blue) and 2.5%, 97.5% quantiles (purple) from Table 4 marked. Location of PPARGC1A is marked in red. Rs8192678 is marked by a red dashed line. Figure S2c Fay and Wu’s H calculated across chromosome 4 using a 1 kbp sliding window. Chromosome 4:22.7–24.9 Mbp is shown with chromosome mean (blue) and 2.5%, 97.5% quantiles (purple) from Table 4 marked. Location of PPARGC1A is marked in red. Rs8192678 is marked by a red dashed line. (ZIP 841 kb

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Schematic of exclusions for the Atherosclerosis Risk in Communities (ARIC), Cardiovascular Health Study (CHS) and Framingham Heart Study (FHS). (DOC 132 kb