J Integr Plant Biol. ›› 2021, Vol. 63 ›› Issue (11): 1937-1951.DOI: 10.1111/jipb.13172

• Functional Omics and Systems Biology • Previous Articles     Next Articles

A global alfalfa diversity panel reveals genomic selection signatures in Chinese varieties and genomic associations with root development

Lin Chen, Fei He, Ruicai Long, Fan Zhang, Mingna Li, Zhen Wang*, Junmei Kang* and Qingchuan Yang*   

  1. Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China

    These authors contributed equally to this work.
    *Correspondence: Zhen Wang (wangzhen@caas.cn); Junmei Kang (kangjmei@126.com); Qingchuan Yang (qchyang66@163.com, Dr. Yang is fully responsible for the distribution of all materials associated with this article)
  • Received:2021-05-09 Accepted:2021-09-03 Online:2021-09-06 Published:2021-11-01

Abstract: Alfalfa (Medicago sativa L.) is an important forage crop worldwide. However, little is known about the effects of breeding status and different geographical populations on alfalfa improvement. Here, we sequenced 220 alfalfa core germplasms and determined that Chinese alfalfa cultivars form an independent group, as evidenced by comparisons of FST values between different subgroups, suggesting that geographical origin plays an important role in group differentiation. By tracing the influence of geographical regions on the genetic diversity of alfalfa varieties in China, we identified 350 common candidate genetic regions and 548 genes under selection. We also defined 165 loci associated with 24 important traits from genome-wide association studies. Of those, 17 genomic regions closely associated with a given phenotype were under selection, with the underlying haplotypes showing significant differences between subgroups of distinct geographical origins. Based on results from expression analysis and association mapping, we propose that 6-phosphogluconolactonase (MsPGL) and a gene encoding a protein with NHL domains (MsNHL) are critical candidate genes for root growth. In conclusion, our results provide valuable information for alfalfa improvement via molecular breeding.

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