If you study Bryophytes or Gymnosperms, you should better take gametophytes.

See: Wu, R. L., O’Malley, D. M., & McKeand, S. E. (1999). Understanding the genetic architecture of a quantitative trait in gymnosperms by genotyping haploid megagametophytes. Theoretical and applied genetics, 99(6), 1031-1038.

For angiosperms - just young true leaves (from seedlings - for an example).

Usually, I will choose young leaves, fresh or silica gel dried, which is easy for sampling. If it is not really necessary, I will not choose seeds, root or fruit. Especially for tree species, lysis the sample at 65C for more than one hour might be necessary.

Good luck.

The majority of existing DNA extraction methods rely on long incubation and multiple precipitations or commercially available kits to produce contaminant-free high molecular weight DNA.

The extraction of good quality DNA with a high yield is a limiting factor in plants’ genetic analysis. DNA quality from each line should be consistent to allow a proper genetic analysis from several plant individuals. High quality of DNA is characterized by predominantly high molecular weight fragments with an A260/280 ratio between 1.8 and 2.0 and the lack of contaminating substances, such as polysaccharides and phenols.

Article Comparison of three genomic DNA extraction methods to obtain...

Thank you for your responses @Alex Ignatov , @Hong-Guang Zha , @Mohammed Hamada Musleh

Honestly, whatever part of the plant is softest and easiest to grind up. Nothing too waxy (some leaves) or oily (like seeds) or mostly dead (bark). Unless is something very easy to get DNA out of (think a soft leaf like spinach), I'd use either a plant-specific DNA extraction kit or an phenol-chloroform extraction protocol. Good luck!

Thanks much @ https://www.researchgate.net/profile/Katie_Burnette

Hi Ananya Phukan

usually, i take softest and easiest part from plant to grind such as leaves and you can use phenol-chloroform extraction protocol or DNA extraction kit

Good luck

root hair and young leaves

I will rather work on soft leaf

An active replicating site (root tips, flower buds, young leaves, stem tips, spores, young gametophytes or sporophytes etc.) Is considered the best.

PS: Sometimes, you might be fortunate to get the best from an old tissue.