Potential Connections Between Sorghum Traits and Gene Functions

Madison Tunnell Author

07/28/2020 Added

28 Plays

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Finding gene-trait connections in the sorghum genome using GWAS and Phytozome.

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[00:00:01.776]Hello, my name is Madison Tunnell
[00:00:03.690]and today I will be presenting
[00:00:05.010]my poster on Potential Connections
[00:00:06.550]Between Sorghum Traits and Gene Functions.
[00:00:12.706]Sorghum is a drought-tolerant plant,
[00:00:14.515]making it an effective crop worldwide,
[00:00:16.596]especially in Africa and Southeastern Asia
[00:00:18.926]where it makes up 50 percent
[00:00:20.526]of cereal grains consumed.
[00:00:22.812]Genome-wide association studies,
[00:00:24.696]also known as GWAS,
[00:00:26.508]search the entire genome of many
[00:00:28.318]individuals at once for various SNPs,
[00:00:30.548]or “snips,”
[00:00:31.218]that are associated with certain traits.
[00:00:34.112]The research presented here is part
[00:00:35.505]of an ongoing research project using GWAS
[00:00:37.935]to identify loci that will be of use
[00:00:40.035]for future plant breeding
[00:00:41.445]and genetic advances for sorghum.
[00:00:44.857]GWAS has already been performed by
[00:00:46.977]Ravi Mural on 304 sorghum individuals
[00:00:49.687]for 234 phenotypic traits
[00:00:51.882]with the MVP package in R.
[00:00:54.395]The 29 most significant associated markers
[00:00:56.885]were then identified and handed
[00:00:58.598]down for this project.
[00:01:00.377]As a side note,
[00:01:01.387]when “window” is mentioned,
[00:01:02.897]it means an area of a chromosome ranging
[00:01:04.785]from one to several million
[00:01:06.326]nucleotide bases long.
[00:01:08.613]The data was presented in an excel file
[00:01:10.553]with the chromosome number and
[00:01:11.723]position of the window, the length
[00:01:13.384]of the window, the number of SNPs in
[00:01:15.454]the window, and the most significant SNP.
[00:01:19.956]A second disclaimer is that every window
[00:01:22.226]had at least two genes to reference,
[00:01:24.266]so this presentation will go
[00:01:25.732]through only one window as an example.
[00:01:28.077]The process was the same for every window.
[00:01:31.206]The first step was to use JBrowse in
[00:01:33.335]Phytozome to search for the selected window.
[00:01:35.959]For windows that were only one base long,
[00:01:37.735]genes directly to the left
[00:01:39.055]and right were used.
[00:01:40.769]For windows with more than twelve genes,
[00:01:42.499]as shown in figure 1,
[00:01:44.259]gene selection was narrowed down to the
[00:01:45.789]most significant SNP in the window and
[00:01:47.719]continued in a similar way as those
[00:01:49.559]with only one base in the window.
[00:01:51.714]This is shown in figure 2.
[00:01:53.760]The genes surrounding the selected
[00:01:55.880]area were used in the next step.
[00:02:00.205]During step two, the NCBI’s BLAST function
[00:02:03.485]was used with the DNA sequences
[00:02:05.540]from the genes in step one to find genes
[00:02:08.069]in similar species with matching sequences.
[00:02:11.069]These similar genes were searched for
[00:02:13.049]functions, and functions that appeared
[00:02:14.829]multiple times were selected for step 3.
[00:02:17.508]An example of the BLAST
[00:02:18.528]results is shown in figure 3.
[00:02:23.518]The third step used UNIPROT’s database,
[00:02:26.386]shown in figure 4,
[00:02:27.952]to search for functions found in step two.
[00:02:30.657]This was to gain a better understanding
[00:02:32.367]of the functions to assist in step four.
[00:02:37.451]In the fourth and final step,
[00:02:39.504]each function identified was compared
[00:02:41.264]to the phenotypic results.
[00:02:42.944]If there was a plausible connection,
[00:02:44.474]then the gene function and phenotypic
[00:02:46.194]trait were considered a match.
[00:02:47.928]For example, the
[00:02:48.978]CEN-like protein shown in figures 3 and 4,
[00:02:51.860]which switches from shoot to inflorescence
[00:02:53.720]growth, would likely match with the
[00:02:55.350]Boyles Days to Anthesis (or flowering)
[00:02:57.880]phenotype, but would not match to the
[00:03:00.370]Morris Testa Tannins (or seed coat
[00:03:02.170]pigmentation) phenotype. Each
[00:03:04.720]potential function was matched in this way.
[00:03:09.153]After completing steps one through four for
[00:03:11.593]every window and potential gene function,
[00:03:13.844]a total of 17 out of the 29 windows
[00:03:16.245]had connections between the gene
[00:03:17.805]functions and phenotypic traits.
[00:03:20.000]Most of these windows had one to ten
[00:03:21.570]matches, but the maximum was
[00:03:23.090]86 out of 151 phenotypic traits matched.
[00:03:27.432]There were a total of 12 windows with
[00:03:29.302]no connections, but two of the windows
[00:03:31.206]had no gene functions to continue with,
[00:03:33.402]so these ended at step two.
[00:03:36.728]The reason these two windows,
[00:03:38.223]windows 8 and 14, had no gene functions
[00:03:40.983]is because the similar genes for these
[00:03:42.704]windows were uncharacterized as of July 2020
[00:03:45.696]and have unknown functions.
[00:03:48.049]For the other ten windows with no connections,
[00:03:50.169]there could still be connections that were
[00:03:52.039]not found within this study.
[00:03:54.520]These results will provide potential
[00:03:56.029]connections to the larger
[00:03:57.249]research project this is a part of.
[00:03:59.501]This study will provide more areas
[00:04:01.885]of the sorghum genome that can be used
[00:04:03.705]to advance plant breeding and genetics
[00:04:05.409]to fit sorghum lines to a
[00:04:06.901]desired environment.
[00:04:09.132]I wish to say thank you to the
[00:04:10.683]University of Nebraska-Lincoln and the
[00:04:12.903]Center for Root and Rhizobiome Innovation
[00:04:14.919]for allowing me this wonderful
[00:04:16.240]research opportunity. I also wish to thank
[00:04:19.010]Dr. Schnable for inviting me into his lab
[00:04:21.226]and assisting me throughout the summer,
[00:04:22.796]and to Ravi Mural who allowed me to be a
[00:04:24.878]part of his research project.
[00:04:26.428]Thank you!

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Potential Connections Between Sorghum Traits and Gene Functions

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