Developing SNPs and strategies for genomic analysis in alfalfa

Authors: MEDINA, CESAR - Washington State University; Yu, Long-Xi

Submitted to: Book Chapter
Publication Type: Book / Chapter
Publication Acceptance Date: 6/7/2021
Publication Date: 7/18/2021
Citation: Medina, C., Yu, L. 2021. Developing SNPs and strategies for genomic analysis in alfalfa. In: Yu LX., Kole C., editors. The Alfalfa Genome. Compendium of Plant Genomes. Springer. Cham, Switzerland. pp.159-175. https://doi.org/10.1007/978-3-030-74466-3_10.
DOI: https://doi.org/10.1007/978-3-030-74466-3_10

Interpretive Summary: Alfalfa is a major forage crop around the world and is the third most valuable field crop produced in the U.S. Abiotic stresses such as drought and high salinity affect alfalfa production resulting in severe economic losses. Genetic improvement in alfalfa has occurred at a slower pace than in other crops. Conventional breeding approaches have not exploited the full yield potential. The use of molecular tools such as marker-assisted selection (MAS) and genomics-assisted breeding (GAB) can accelerate the breeding process. As advances of next generation sequencing technologies, high density of DNA markers become popular and provide important platforms for discover genetic factors that influence production and quality of alfalfa. In this chapter, we discussed bioinformatics pipelines for developing DNA markers and associated strategies to utilize DNA markers for genetic improvement of alfalfa.

Technical Abstract: Continued advances in plant breeding require of innovative breeding strategies such as marker-assisted selection and genomic selection. New technologies of next generation sequencing provide efficient genotyping strategies such as genotype-by-sequencing or RADseq which can generate high density single nucleotide polymorphisms (SNPs) at the whole genome level. However, in autotetraploid alfalfa, developing markers requires analysis of allele dosage as it can affect genotyping accuracy. Similarly, different models are required for genome-wide association studies to overcome the genome complexity in autotetraploid genomes. In this chapter, we summarize the recent progress on different methodologies for effectively handling SNPs genotyping, marker development, allele dosage, association mapping and genomic selection in alfalfa. As recent advances in sequencing technology, the cost of sequencing is reduced and sequencing the whole genomes becomes realistic in polyploids including cultivated alfalfa. Several alfalfa genomes have been sequenced and the sequence assemblies of two cultivars of alfalfa at the chromosome level have been published in last year, providing reference genomes for sequence alignment and genotype calling in tetraploid alfalfa. Toward this end, in this chapter, we also reviewed bioinformatics pipelines for SNP discovery and genotyping.