I am almost 2 years in to my PhD, in the biological sciences. After completing a pilot study in my area, my supervisor has suggested that I try and publish it. He thinks that a lower impact journal would be appropriate for this work, whilst my current and future studies might have a chance in a higher impact journal down the line. I am a little worried however about if my paper gets rejected, how would I explain this in the viva once I submit? This study will form my first chapter. Any advice is greatly appreciated. Thank you

Most people have their papers rejected, I don't think it would have any bad effects for your Viva. If it is rejected from one journal you could try another (I think I got told once that a very high percentage of published papers had been rejected from other journals). Unless you are on a specialist PhD you don't need to have your chapters published before your Viva, in fact I am only planning to put mine forward for publishing once I have submitted as I don't have time to do it before.

Hi Caro, thank you for your reply. Yes I just thought that if my supervisor is advising it then it's worth a try. If it gets rejected should I still keep it as a stand alone chapter, refine it and try again after the viva in your opinion?

I think it would be seen more negatively not trying to publish than being rejected. As already mentioned, everyone has papers rejected, and it's bound to be more likely when you start off. It's also perfectly likely that something that's not accepted as a journal article will make a perfectly good thesis chapter.