Pre-breeding in alfalfa germplasm develops highly differentiated populations, as revealed by genome-wide microhaplotype markers

Authors: MEDINA, CESAR - University Of Minnesota; LIN, MENG - Cornell University; ZHAO, DONGYAN - Cornell University; SAPKOTA, MANOJ - Cornell University; SANDERCOCK, ALEXANDER - Cornell University; BEIL, CRAIG - Cornell University; SHEEHAN, MOIRA - Cornell University; Irish, Brian; Yu, Long-Xi; POUDEL, HARI - Agriculture And Agri-Food Canada; CLAESSENS, ANNIE - Agriculture And Agri-Food Canada; MOORE, VIRGINIA - Cornell University; CRAWFORD, JAMIE - Cornell University; HANSEN, JULIE - Cornell University; VIANDS, DONALD - Cornell University; Peel, Michael; Tilhou, Neal; Riday, Heathcliffe; BRUMMER, CHARLES - University Of California, Davis; Xu, Zhanyou

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/23/2024
Publication Date: N/A
Citation: N/A

Interpretive Summary: Alfalfa, or lucerne, is known as "the queen of forages" due to its high productivity, nutritional value for animal feed, and nitrogen-fixing ability. It ranks as the USA's third most economically important crop. However, alfalfa biomass yield improvements have been slow in the past 50 years compared with corn and soybean partly due to the complex genetic composition, with multiple copies of each chromosome. In addition, current breeding pools also have a low level of genetic diversity, which has hampered the genetic improvement of crops via plant breeding. To discover new and superior genes to improve alfalfa biomass yield and resilience, forage breeders from North America worked collaboratively to evaluate global alfalfa genetic resources in trials in US and Canada alfalfa planting regions under the project "NE1710/NE2210: Improving Forage and Bioenergy Crops for Better Adaptation, Resilience, and Flexibility". The team of scientists used universal, advanced genotyping technologies to characterize 3,000 genes covering all alfalfa chromosomes. The genotyping platform was developed by Breeding Insight (BI) and allowed the team to conduct diversity analysis and to seek new genes. The team found highly diverse combinations of genetic markers that could find relationships between alfalfas from different geographical pools. Work here will provide the basis for protecting diversity in alfalfa germplasm during breeding. The resulting populations developed in this project offer novel alleles that will allow alfalfa breeding programs to create diverse and adapted new cultivars, breaking the alfalfa yield bottleneck.

Technical Abstract: Plant genebanks contain large numbers of accessions that likely harbor useful alleles or genes absent in commercial plant breeding programs. Broadening the genetic base of commercial alfalfa germplasm with these useful genetic variations can be accomplished by screening the extensive genetic diversity in germplasm collections and enabling maximal recombination among selected genotypes. In this study we surveyed the genetic diversity and differentiation of germplasm pools selected in northern US latitudes (USDA Plant Hardiness Zone seven or less) originating from Eurasian germplasm. The germplasm evaluated here included four BASE populations (C0) from different geographical origins (CASIA, EURO, OTTM, SYBR), 20 cycle-one populations (C1) generated from each of the four BASE populations selected in five locations in the USA and Canada, and four commercial cultivars. A panel of 3,000 SNP Diversity Array Technologies (DArTag) markers harboring ~10,000 microhaplotypes were used to quantify genetic diversity and population structure. PCA and DAPC identified significant population structure among the alfalfa populations based on their geographical origin, while the check cultivars formed a central cluster. Inbreeding coefficients (FIS) ranged from -0.06 to 0.04, and 23 out of 28 populations had negative FIS values, indicating an excess of heterozygotes. Interpopulation genetic distances were calculated using Rho and analysis of molecular variance (AMOVA) parameters. Pairwise population Rho values ranged from 0.0071 to 0.3019. All BASE populations had the lowest Rho values compared to C1 populations and check cultivars. AMOVA found high variance among individuals within populations and low variance between populations. Variation among population was highest among check cultivars and lowest in BASE populations at 14.6% and 8.6% of total molecular variation, respectively. This study shows that BASE populations have high gene diversity, low interpopulation distances, and minimal inbreeding which is required for base-broadening selection.