Transcriptional variation in cis and trans, genetics of quantitative traits. Anne Genisell, Rita Graze & Lauren McIntyre UG Florida Rita Graze, Maria Persianinova & Olga Barmina Artyom Kopp & Ryan Bickel

Transcriptional variation in cis and trans QG of divergence between species QG of variation within species

cis or trans? allele specific? Agilent 60 bp Splicing Arrays, 8 R I Lines:

1. Genetic variation  2. Infinitesimal model  1 cis; zillion trans. 3. ‘Large trans-effect’  model (g: P0, P1, O0, O1) 3685 cis trans cis-by-trans Infinitesimal  Large-effect  Overlap cis or trans? allele specific?

Morley et al. 2004: 14 human families; 3,554 genes with significant genetic variation; 984 QTLs  19% cis, 78% trans, 3% both; (co-localized) An average QTL accounts for ~50% of variation. Power? LOW (5%)  overestimation VARIABLE  explains co-localization? cis or trans?

hybrids Wittkopp, Haerun, Clark, 2004 mel sim cis or trans? allele specific?

Genes with mismatches: O S O*S mau sim hyb Michalak & Noor 2003 cis or trans? allele specific?

False positive False negative GCRMA12.5%61.8% MAS %65.6% ln(PM)18.7%59.9% ln(PM/ MM) 18.4%57.2% Norm.cistranscis & trans GCRMA 381 MAS ln(PM)281 ln(PM/ MM) 7695

Transcriptional variation in cis and trans QG of divergence between species QG of variation within species

Divergence in sex comb tooth number. D. simulans D. mauritiana Chromosome III: LOD cM Sex Comb Tooth Number traAntp Reproduced from: True et al. (1997)

Introgression line mapping e+e+ P{lacW}76C P{lacW} [76C] e [93C] e+e+ + D. simulans D. mauritiana Obtained recombinants between two flanking visible markers: 62 nearly isogenic lines :

Introgression line mapping results Marker Type III SS F valuePEffect c SE c t value c 93C (ebony) a X A (Scr) b X P{lacW}76C a X C (Dip2) b X B (rdgC) b D (Ten-m) b Sig. Interactions

Comparing expression T1 & T2 pupal legs Pupal legs were collected at 16h post pupariation For each leg and each species, legs from multiple males were pooled into 3 biological replicates each. The mRNA was amplified and hybridized to Drosophila 2.0 Affymetrix GeneChips ® T2 D. mauritiana T D. simulans T T2

Combining mapping & array results: Gene Band Biological Process Molecular Function FDR m,g P m P g CG E1 Unknown.05 m,g <.0001 m <.0001 g CG D8 Transport Transporter activity.05 m,.1 g <.0001 m.0143 g ara 69C8 Morphogenesis Transcription Factor.05 m,.1 g.0026 m.0068 g kal-1 95E1 Cell adhesion Fibronectin type III.05 m,g.0014 m.0014 g CG E8 Unknown.05 -,g ---<.0001 g CG E6 Unknown.1 -,g g CG E4 Unknown Takeout family.2 m, m --- CG A11 Unknown.2 m,-.03 m --- &

We examined five insertions in or near CG2791, two affect sex comb number and morphology. Is CG2791 a sex comb gene? dsx CG2791 Os-C 1.P{SUPor-P}KG01932 reduces tooth number and has weakly penetrant effects on the sex comb PBac{5HPw [+])A146 reduces tooth number slightly and causes curving in the top portion of the sex comb.

Tibia Metatarsus T2 CG2791 is expressed in T1 and not in T2 Tarsus 24 hours post-pupariation T1 CG2791 is expressed on the ventral anterior surface of T1, but not T2. sex comb PBac{GAL4D, EYFP} CG2791 PL00285 /UAS-LacZ

What’s the proof? - have gone all the way from between species morphological differences  to QTLs  to fine-mapping  to the gene. Transformation? (position effect) Gene replacement (not D. melanogaster) Modification of allele-specific expression?

Transcriptional variation in cis and trans QG of divergence between species QG of variation within species

Building a genotype to phenotype map

bab1bab2 Low LD (200 b) enables precise association inferences

AbdBDsxF bab Yellow Gene functioning might be assayed at the right time in the right tissues…

AbdB DsxF Yellow bab Snp1 Snp2Snp3Snp4Snp...indel1 bab variation Phenotype … to build the genotype to phenotype map.