Genomic admixture | Introduction to genomics theory | Genomics101 (beginner-friendly)

[@mohammadj.shamim9342]

Thank you so much. It was very informative. I really enjoyed watching it. You are a great blessing, professor. I think this video needs to be grouped with structure and fat playlist videos where you practically showed us in plunk and structure. Thank you so much.

[@GenomicsBootCamp]

Thanks! KZbin gives limited possibilities to create complex and inter connected structure among videos. I will try to make these connections, but perhaps an other framework will be also needed.

[@caroline2627]

Thank you so much! This is very helpful information for my thesis :) Very clear and informative.

[@tapiwamagwaba8107]

informative video. It would be interesting to see how this can be implemented I PLINK from SNP data

[@GenomicsBootCamp]

Hi, I don't think PLINK has a direct implementation, but you an try out the STRUCTURE software, as described on ths channel. Also, there is a software called ADMIXTURE and other software that does such calculations.

[@РоманПерфильев-ц7ь]

Спасибо большое за ваши видео

[@GenomicsBootCamp]

Пожалуйста!

[@saifulanwar450]

Thank you so much, Sir. I'm pleased to be able to watch this video. It adds a lot to my insight. I have questions: 1) So this analysis can be used to apply to the individual selection of purebred cattle or individuals whose genetic composition is not included in the population group? In this way, can we determine the genetic composition standards of certain breeds? As in the samples at 8:21 and 9:33 minutes, can we exclude them from the population group? 2) what does the parent population? does it always have to be purebred? if there is a fixed population as a result of crossbreeding (a mixture of several breeds), can it be used as a factor in the parental population? 3) If the population we are testing is the result of crossing 4 breeds, because there are no pedigree records and we only use 3 parental populations, is it possible that the genetics of the other breeds are unknown in the population we are testing? 4) I would really appreciate it if you could explain further about the value of K (is it like K=5, K=7, etc.?), how to determine it, and interpret it, in another session?

[@GenomicsBootCamp]

Hi! 1) Yes, if your goal is to identify these individuals, you can use admixture to do so. For example if you want to identify crossbreds in a supposedly purebred population. 2) Just to clarify: the "parental" population is a bit misleading, these animals must not be literally the parents of the crossbreds. Just from the breeds involved in the crossbreeding. For example in a Holstein x Fleckvieh cross, the purebred grsoups should be pure Holstein and pure Fleckvieh. So to confirm, they should be purebred. 3) In a way this is the continuatio of question 2. If you can not identify all parenal populations, you can include what you have, but specify a higher K value. e.g. in your example, you have your crossbreds, and he 3 knownd purebred populations. You sepcify K = 4, with an expectation that the 3 purebred clusters into one population each, and the crossbreds are a mixture of these 3 and the other 4th component. This is already a very complex situation already, so it will likely will not be this clean. 4) Yes, the K values are a returning question for clarification. Will see what can I do.

[@lucasf.c.y.dossoukpongan4684]

Thanks so much Professor, can I have the database for the sheep populations of Ethiopia in order to practice your teaching.

[@GenomicsBootCamp]

I am not sure which data are you referring to, but go to the WIDDE data base and you can get plenty. From Ethipoia and elsewhere. widde.toulouse.inra.fr/widde/