The genetic basis and analysis of simply inherited traits: PBG430/530 Plant Genetics The genetic basis and analysis of simply inherited traits: Examples including domestication, economic impact, +,+,+ Phenomena particularly important in plants: Examples including self-incompatibility, polyploidy , +,+,+ Genetics tools for manipulating plants (and other organisms): Examples including linkage mapping, genome sequencing, GMOs, CRISPR-CAS9, epigenetics, +,+,+ http://www.nwfoodnews.com/2011/02/18/meet-the-sugar-beet/

Barley domestication traits, the genes, and the mechanisms Locus/alleles Phenotype Mechanism Btr1,Btr2 Shattering/retention Loss of function deletions Vrs1 2-row/6-row Nud Hull adherence Vrn1, Vrn2, Vrn3 Growth habit Loss of function deletions Ppd1, Ppd2 Flowering time Pourkheirandish et al., 2015

~758 Mb (the haploid (n) genome size, by convention) Economic impact and GMO: Hybrid sugarbeet seed production in the Willamette Valley of Oregon - gene flow with organic table beet (Greg Loberg West Coast Beet Seed) Beta vulgaris 2n = 2x = 18 ~758 Mb (the haploid (n) genome size, by convention)

Sugarbeet seed production in the Willamette Valley – 2017 (ACH seeds) (Harris seed ) Sugarbeet seed production in the Willamette Valley – 2017 ~ 90+% Roundup Ready ~ $2,000/acre (gross) Controlling gene flow to organic table beet Spatial separation and pinning RR sugarbeet - females only For more on sugarbeet seed production see CSS450/460

Phenotype: susceptible Seed production: Blue = male Red = female Seed production: Blue = male Red = female Genotype: RR Phenotype: resistant Genotype: 00 Phenotype: susceptible http://www.crystalsugar.com Pair of homologous chromosomes Each missing R gene Showing only 1 pair of the 9 pairs of chromosomes (2n = 2x = 18) Pair of homologous chromosomes Each has R gene Showing only 1 pair of the 9 pairs of chromosomes (2n = 2x = 18)

R R The “R”* locus (same position on each homologous chromosome) 2 copies of the R gene; each copy is one allele The R locus (same position on each homologous chromosome) 2 copies of the absence of the R gene; each copy is one allele More on the transgene conferring resistance to glyphosate

meiosis meiosis R R Male gamete R Female gamete

select a resistant type (if you want); R0 All F1 progeny plants are R0 Resistant (R is dominant to 0) R RR R0 00 F2 plants 3 Resistant: 1 susceptible 1 RR: 2 R0: 1 00 RR, Rr: select a resistant type (if you want); deal with gene flow (if you have to)

Phenomena: Polyploidy Diploid (2n = 2x) to polyploid (2n = _x) - all in the wheat “family” VAVA VAVAVBVB VAVAVBVBVDVD 2n = 2x = 14 30,000 genes Emmer wheat 2n = 4x = 28 60,000 genes Durum wheat 2n = 6x = 42 90,000 genes Bread wheat 1 pair homologous chromosomes 0 sets of homoeologous chromosomes AA 2 pairs of homologous chromosomes 2 sets of homoeologous chromosomes AABB 3 pairs of homologous chromosomes 3 sets of homoeologous chromosomes AABBDD A A B B A A A A B B D D

Ploidy does not equal horsepower 2X 8X Ploidy does not equal horsepower

Genetics tools: CRISPR-CAS9 Clustered Regularly Interspersed Short Palindromic Repeats Genome editing: delete/add/modify genes Target gene sequence and information Cas 9 nuclease enzyme Guide RNA (gRNA) A technical explanation (optional for now): http://www.sigmaaldrich.com/technical-documents/articles/biology/crispr-cas9-genome-editing.html#what-is An overview from an inventor (required): https://www.youtube.com/watch?v=TdBAHexVYzc

Genetics tools: CRISPR-CAS9 A Naked (Barley) Promise? Golden Promise barley With a Nud gene knock-out Taketa et al., 2008