Malcolm C

This is where I will capture my progress on this project.

I will also be working on the 13 genes Allan gave us.

The class has already completed 4 SSR primer designs (LDOX, CHS, StSy, and F3H).

Results from Blueberry 454 Scaffold Searches from Grape (given to us by Allan Brown)
AOMT Scaffold 00796

1. Forward Primer GAGCTCTTGGATGCTCCATACT & Rev Primer CCTCATAATTTTTGGTCTTCGC (taa) x6 PCR product = 137 bp
2. Forward Primer TATCCCATGTTTTGGCTAATCC & Rev Primer TTTGCTTTTCAATCGGGAAC (tc) x9 PCR product = 261 bp

AOMT scaffold 01781

1. Forward Primer GGCGACTGTGTCTTTCAGTAAA & Rev Primer TAGGATTTCGAGGAGGAGAGGT (ct) x7 PCR product = 136 bp
2. Forward Primer ATAAACAGGTAAACCGAACCGA & Rev Primer CCGATTAAATTGGAGCAGTAGC (tg) x7 PCR product = 262 bp

ANPER scaffold 00666

1. Forward Primer TTTCTATCTCTCTCGCCGTCAT & Rev Primer GTTTTCTCACCTTGTTTTTGCC (ct) x21 PCR product = 219 bp
2. Forward Primer CCGTTTCGATCTCTCTCTCAGT & Rev Primer CATCCCTAGATCTGACACCACA (tc) x14 PCR product = 278 bp

CHI scaffold 03186

1. Forward Primer TACATCTTGAGGGGCAGTTTTT & Rev Primer GTGGAGTGTGGGATATGGATTT (tc) x5 PCR product = 121 bp
2. Forward Primer ACGTGGTCCAATCTAACCTCAC & Rev Primer TAGTAAGTGGAGGCCGGTAAAA (cttt) x4 PCR product = 288 bp

DFR scaffold 03132

1. Forward Primer TACATCTTGAGGGGCAGTTTTT & Rev Primer GTGGAGTGTGGGATATGGATTT (tc) x5 PCR product = 121 bp
2. Forward Primer ACGTGGTCCAATCTAACCTCAC & Rev Primer TAGTAAGTGGAGGCCGGTAAAA (cttt) x4 PCR product = 288 bp

F3'H scaffold 01438

1. Forward Primer CAGTGGTACAGTGGTGGATGAC & Rev Primer ATTCCCTTTCTCTTCCCATTTC (ag) x7 PCR product = 152 bp
2. Forward Primer ATACCAATCCATAGTCTCCCGA & Rev Primer TCAGTTGTGTTTTTCAGTTGGG (ta) x7 PCR product = 279 bp

FLS scaffold 00142

1. Forward Primer CAATTATACCCTTCCTGTCCCA & Rev Primer GAATGGATGAAAGGAACCCATA (ag) x8 PCR product = 214 bp
2. Forward Primer CTAGCTCTCCCTCTCTCCCTCT & Rev Primer GTGGTACTCCATATCCATGCCT (ct) x8 PCR product = 295 bp

FLS scaffold 00374

1. Forward Primer TGAGCATCATTGCCAGAGTAGT & Rev Primer GGATTTCATTCCAAGAGATTGC (ct) x6 PCR product = 295 bp
2. Forward Primer TAGATTATCCGGGGAATCATTG & Rev Primer GATTCTCATGACAAGCCAGTTG (tc) x6 PCR product = 275 bp

MYBA1 scaffold 03500

1. Forward Primer GCGAGGATGGAAATATATACGG & Rev Primer GCTTCATAAGCTGCTAGGCAAT (ag) x8 PCR product = 222 bp
2. Forward Primer GCGAGGATGGAAATATATACGG & Rev Primer GCTTCATAAGCTGCTAGGCAAT (ttat) x5 PCR product = 222 bp

MYCA1 scaffold 00278

1. Forward Primer CAGTATTTGAGCCGGAACCTAC & Rev Primer CGTACAGAGTTTCGCACAAAAG (ct) x7 PCR product = 268 bp
2. Forward Primer TAGTGGGAACGAGTCGTCTTTT & Rev Primer AGTTGGTGCCCTTTTATGAAGA (at) x6 PCR product = 195 bp

MYCA1 scaffold 00554

1. Forward Primer GGCTAAAACCCTAGTTGCCTTT & Rev Primer GGGTGTACTGAGAACCGAAGTC (tc) x6 PCR product = 157 bp
2. Forward Primer CCCAAAAGAAAATACCTGGACA & Rev Primer GGAGCTTGGACCTAAAAGGATT (ga) x8 PCR product = 260 bp

UFGT scaffold 00304

1. Forward Primer TGAACTACCAAAATGGGACAGA & Rev Primer NGACGGAGCACATCCTACTACA (ag) x10 PCR product = 207 bp
2. Forward Primer CCCCAAATTCAGATCAAAGAAG & Rev Primer CTTATCTCTGCCCACCTACACC (ag) x12 PCR product = 230 bp

UFGT scaffold 01120

1. Forward Primer TGTGTGTGTGTAGTGTGGTCGT & Rev Primer AAGAGAGAGGGGTCCTGAAAAC (ct) x11 PCR product = 132 bp
2. Forward Primer TAAGCTACAGTACCTCGCCACA & Rev Primer AAGGATATGCCGACGAGTCTTA (tc) x6 PCR product = 196 bp

For the second half of the semester, we focused on finding ESTs of our genes using the [ Washington State University Vaccinium genome database] as well as the Towson State University Blue Berry Genome database using 454 sequencing.