Abstract:

With the rapid development of high-throughput sequencing technology， the sequencing cost has been greatly reduced， and the sequencing speed and data quality have been significantly improved. These developments greatly promote the in-depth study of the alfalfa （Medicago sativa） genome， and thus provide important basic information for the development of molecular markers for the association of different traits in alfalfa. Insertion/deletion （InDel） polymorphic markers have attracted great attention because of their wide distribution， high density， genetic stability， and high reproducibility， but research about them and their application in alfalfa are still very limited. In this study， based on genome resequencing data of 80 alfalfa germplasm lines sourced from China and abroad， we explored the InDel locus by comparing with the reference genome sequence of alfalfa “Zhongmu No.1”， and identified InDel markers related to high-protein and high-yield traits. It was found that of 40 markers identified on a genome-wide scale， 29 polymorphic markers were successfully categorised with a polymorphism ratio of 72.5% after validation by polymerase chain reaction （PCR）. Notably， markers designated InDel_25 and InDel_39 are particularly useful for the identification of high-yield and high-quality alfalfa germplasm lines， respectively. It is anticipated that the InDel markers identified in this research will be applied in traditional breeding programs， thereby accelerating the development of new alfalfa varieties with enhanced yield and quality.

Key words: alfalfa, InDel molecular markers, yield, quality