7.10 lecture 1: crops from the past are our crops for the future Flashcards
Key points in relation to maize domestication
Developmental traits are generally those selected for
Remember that much of the work in crop domestication happened over thousands of years by early peoples
Corn is a major source of animal feed in the USA
Changes in 4 or 5 genes ( resulting in diff in 1 in 500 in an f2 cross) were responsible for all the differences between teosinte and maize – could not be certain of exact no. As some genes are quantitative
Original domestication of corn ~9,0000 years ago
Archeologists were able to identify where teosinte was first ground using stone tools – leaving microfossils on the grindstones – allowing scientists to identify differences between teosinte and maize. Microfossils are too small to date by radiocarbon methods so nearby charcoal age was used -> 8700 years ago – matching the prediction from genetic evidence
Hard fruit case is coded for by one gene – removing it from teosinte causes exposed kernels, adding it to maize causes hard covered kernels
Teosinte branching gene causes branching in maize and the alternate gene from corn added to teosinte prevented branching
Both genes are regulatory – they influence the activity of other genes
Early farmers may have utilised teosinte by popping it over a fire – the way we make popcorn today
Maize was domesticated in the southern highlands of Mexico
Zea mays ssp. parviglulmis is the wild ancestor
5310 wild corn cob was found in the Tehuacan valley is ~450 km from the Balsas river valley (where corn was first domesticated)
maize arose from a single domestication event - what is the evidence for this?
Molecular markers can define genetic differences between populations
They are specific to one ecotype
Microsatellites are distributed throughout the genome:
*Microsatellites are repeat sequences in genomic DNA.
*They are the result of DNA polymerase errors during replication.
*Repeat sequences vary in length in different accessions.
*Resulting in variations in DNA length
*Adjacent DNA does not vary.
These markers can be used to build a phylogeny and this was used to identify that the original maize domestication in the Mexican highlands is adjacent to teosinte
Next generation sequencing - sequencing by synthesis with fluorescent detection
Tehuacan162 was sequenced to 1.6x coverage
It was compared to other maize sequenced using principle component analysis
Principle Component Analysis (PCA)
“An orthogonal linear transformation”
transforms the data to a new coordinate system
Tehuacan162 sequence compared to others: 1st principle component analysis graph – this represents the majority of variation in the data (see notes for diagram)
‘landraces’ domesticated (but not through breeding programmes?) observed also - this ‘pre-columbian corn’ was highly specialised to different areas of mexico (see notes for diagram)
see:
Matsuoka, Y., Vigouroux, Y., Goodman, M.M., Sanchez, J.G., Buckler, E. and Doebley, J. (2002) ‘A single domestication for maize shown by multilocus microsatellite genotyping’, Proceedings of the National Academy of Sciences, 99(9), pp. 6080-6084. doi: ?
Pawnee Eagle Corn (an example of pre-columbian corn)
*Pawnee had grown this corn in what is now Nebraska for 600 years.
*They brought seed when exiled from Nebraska to Oklahoma in the 1870s.
*They’d been trying to save it since but by 2004, only 25 seeds remained.
*Eagle corn was recovered by growing it in Nebraska.
*bred for the eagle silhouette on lower kernels (see photo)
Why might Pawnee Eagle corn not grow in Oklahoma?
We don’t know
But we can speculate
Maize was bred for growth in specific regions across the Americas
see: Swarts, K., Gutaker, R.M., Benz, B., Blake, M., Bukowski, R., Holland, J., Kruse-Peeples, M., Lepak, N., Prim, L., Romay, M.C., Ross-Ibarra, J., Sanchez-Gonzalez, J.J., Schmidt, C., Schuenemann, V.J., Krause, J., Matson, R.G., Weigel, D., Buckler, E.S. and Burbano, H.A. (Year) ‘Genomic estimation of complex traits reveals ancient maize adaptation to temperate North America’,
Turkey Pen maize
~1850 year old maize variety. Cultivated on the Colorado plateau
Higher weather tolerance?
Turkey pen maize had been selected for growth in temperate regions
Tropical, but not temperate corn varieties were significantly different from Turkey pen corn
Turkey pen flowering period is comparatively shorter than most other varieties
Flowering time in maize differs by location and was under selection
Maize has separate male and female flowers - the pollen falls from the male to pollinate the female flowers – self-pollination avoided by male and female flowers maturing at different times on the same plant (97% silks pollinated by neighbouring plants)
see: Monyo, Emmanuel & Banziger, Marianne. (2004). Successful Community-Based Seed Production Strategies. CIMMYT: International Maize and Wheat Improvement Center, Manuals.
https://www.researchgate.net/publication/46471766_Successful_Community-Based_Seed_Production_Strategies
Where did the ‘temperate’ alleles come from?
Surprising observations have been made considering it was a single domestication event
*disparities between genetic and geographic overlap between maize and parviglumis.
*mexicana ancestry is found far outside its current range, including in ancient maize from New Mexico and modern samples in the Peruvian Andes.
*Individual alleles were apparently selected in modern maize.
Alleles from Mexicana at ZmPRR37a are found in up to 89% of all maize
ZmPRR37a is involved in the circadian clock controlled flowering pathway - It controls flowering under long-day conditions
The Inca Empire was underpinned by experimentation in agriculture
See: Inca cultivation with fire-hardened digging sticks. Drawing from Nueva corónica y buen gobierno by Felipe Guamán Poma de Ayala, 17th century; in the Royal Library, Copenhagen.
https://www.britannica.com/topic/Inca#/media/1/284517/233
Also see photo of Moray crop (in lecture) showing an testing site located within the Incan Empire
How molecular markers work: example: branching traits
Each generation chromosomal regions reshuffle
see lecture diagram:
- LBIL influences internode length in primary branch
-LIBN influences no. Of branches
-STAM influences no. Of male spikelets in flowering
Identify members of the F2 with either a maize or teosinte branching arrangement
Ask if those plants have a difference in distribution of molecular markers
^ identify differences in molecular marker distribution
Quantitative trait locus (QTL) is a genomic region associated with a specific phenotype
*A QTL is a region of DNA associated with a trait.
*Traits vary in degree. They may be attributed to polygenic effects.
*QTLs differ from Mendelian segregation, where traits segregate in predictable ratios.
lecture diagram shows that in F2 generation a shift away from 1:2:1 ratio is visible on chromosome 8
^ In an area that impacts level of expression
QTLs associated with maize domestication:
tb1 - plant architecture
zfl2 - ear phyllotaxy
tga1 - fruit case development
Introgression can refine genomic location - Molecular markers are greatly accelerated by breeding programmes
in backcrosses – markers accelerate breeding programmes:
Cross breeding to introduce disease resistance into a high yielding variety
Using backcrossing to improve yield once resistance traits are expressed
Genome sequence data are available for many important crop species
Advances in genomics technologies facilitate breeding for complex traits
*Genome sequences are available for many crop species
*Molecular breeding and mapping tools are available
*Genome-wide association studies (GWAS) help match genes to traits
Genome-wide methods allow the identification of genes associated with complex traits, such as yield or water use efficiency
GWAS process
GWAS process:
1 - phenotype analysis
2 - genotype analysis
3 - association analysis
4 - gene discovery
The genome wide approach allows hundreds of genes with small effects to be identified
*In maize, grain yield is correlated with leaf angle and size.
*GWAS has revealed hundreds of single-nucleotide polymorphisms (SNPs) associated with these traits, providing invaluable information for breeders.
see SNPs identified by GWAS in: Tian, F., Bradbury, P.J., Brown, P.J., Hung, H., Sun, Q., Flint-Garcia, S., Rocheford, T.R., McMullen, M.D., Holland, J.B., and Buckler, E.S. (2011). Genome-wide association study of leaf architecture in the maize nested association mapping population. Nat Genet 43: 159-162.
Similar studies have led to the identification of genes contributing to other agronomically important traits : e.g. leaf blight tol.
SNPs contribute to resistance to Southern leaf blight:
see diagram from: Macmillan Publishers Ltd Kump, K.L., Bradbury, P.J., Wisser, R.J., Buckler, E.S., Belcher, A.R., Oropeza-Rosas, M.A., Zwonitzer, J.C., Kresovich, S., McMullen, M.D., Ware, D., Balint-Kurti, P.J., and Holland, J.B. (2011). Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population. Nat Genet 43: 163-168.
Branching and domestication : A mutation in a single gene is key for the reduced tillering and increased apical dominance in maize
QTL tb1 associated with plant architecture a transcription factor influencing branching
Quantitative – not always on/off
Teosinte plants typically bear elongated lateral branches at most nodes
Cultivated maize plants generally do not produce many tillers or side branches
A gain-of-function mutation in teosinte branched1 (tb1), encoding a transcription factor, leads to inhibition of side branching
tb1 regulates branching with an on/off function
see: expression patterns and mutant phenotype of teosinte branched 1 correlate with growth suppression in maize and teosinte Lauren Hubbard et al.
In maize the shoot is made up of repeating units called phytomers
Phytomers consist of a leaf, a node, an internode and an axillary meristem
tb1 must be impacting stem cell activation to regulate branching
^ branching varieties (tb1-r) have activated axillary meristems causing side branch development
see: Sanchez, P., Nehlin, L. and Greb, T. (2012) ‘From thin to thick: major transitions during stem development’, Trends in Plant Science, [online] 17(2), pp. 113–121. Available at: https://doi.org/10.1016/j.tplants.2011.11.004
Does TB1 expression differ in maize compared to teosinte?
In cultivated maize, Tb1 mRNA accumulates in axillary meristems
Axillary branches do not expand in cultivated maize – Tb1 must be a repressor of branch expansion
Hypothesis:
Tb1 expression may be absent from teosinte axils
to allow branching to occur
RNA in-situ hybridisation (how to define where a gene is expressed)
disable mRNA using probe, detect by antibody+AP:
- add dicoxigenin-labelled probe
-labelled probe is complementary to gene of interest and sticks to the mRNA - add alkaline phosphatase-conjugated antibody
- An antibody that recognises the label on the probe is conjugated to the enzyme alkaline phosphatase. The antibody+AP sticks to the probe that is stuck to the mRNA - Add chemical that becomes dark purple dye when phosphate is removed - the dye colours the cell.
- if present the phosphate is removed from the AP and as a result the location in the cell where the gene is expressed is dyed purple
Promotor region differs between teosinte and maize
These promoter region differences must account for the difference in Tb1 expression
A gene has a promoter (where RNA polymerase and transcription factors bind)
and 5’ and 3’ untranslated regions (UTRs) to promote translation and mRNA stability
Domestication has created diverging branching patterns
Wheat and rice have been selected for multiple tillers that distribute grain production evenly, with relatively simultaneous maturation
Some cereals have had a strong increase in apical dominance,
suppressing side branching and concentrating seed production on a single, large terminal head as in corn and sunflowers
branching can be beneficial - increased tillering increases yield in cereal crops
it can also be undesirable - branching reduces timber quality by creating knots in the wood
