Chromosome evolution and the genetic basis of agronomically important traits in greater yam

Bredeson, J.V.; Lyons, J.B.; Oniyinde, I.O.; Okereke, N.R.; Kolade, O.; Nnabue, I.; Nwadili, C.O.; Hřibová, E.; Parker, M.; Nwogha, J.; Shu, S.; Carlson, J.; Kariba, R.; Muthemba, S.; Knop, K.; Barton, G.J.; Sherwood, A.V.; Lopez-Montes, A.; Asiedu, R.; Jamnadass, R.; Muchugi, A.; Goodstein, D.; Egesi, C.; Featherston, J.; Asfaw, A.; Simpson, G.G.; Doležel, J.; Hendre, P.; Van Deynze, A.; Kumar, P.L.; Obidiegwu, J.; Bhattacharjee, R.; Rokhsar, D.S.

Welcome to the International Institute of Tropical Agriculture Research Repository

What would you like to view today?

View/Open

Journal Article (560.7Kb)

Date

2022

Author

Bredeson, J.V.

Lyons, J.B.

Oniyinde, I.O.

Okereke, N.R.

Kolade, O.

Nnabue, I.

Nwadili, C.O.

Hřibová, E.

Parker, M.

Nwogha, J.

Shu, S.

Carlson, J.

Kariba, R.

Muthemba, S.

Knop, K.

Barton, G.J.

Sherwood, A.V.

Lopez-Montes, A.

Asiedu, R.

Jamnadass, R.

Muchugi, A.

Goodstein, D.

Egesi, C.

Featherston, J.

Asfaw, A.

Simpson, G.G.

Doležel, J.

Hendre, P.

Van Deynze, A.

Kumar, P.L.

Obidiegwu, J.

Bhattacharjee, R.

Rokhsar, D.S.

Type

Journal Article

Review Status

Peer Review

Target Audience

Scientists

Metadata

Show full item record

Abstract/Description

The nutrient-rich tubers of the greater yam, Dioscorea alata L., provide food and income security for millions of people around the world. Despite its global importance, however, greater yam remains an orphan crop. Here, we address this resource gap by presenting a highly contiguous chromosome-scale genome assembly of D. alata combined with a dense genetic map derived from African breeding populations. The genome sequence reveals an ancient allotetraploidization in the Dioscorea lineage, followed by extensive genome-wide reorganization. Using the genomic tools, we find quantitative trait loci for resistance to anthracnose, a damaging fungal pathogen of yam, and several tuber quality traits. Genomic analysis of breeding lines reveals both extensive inbreeding as well as regions of extensive heterozygosity that may represent interspecific introgression during domestication. These tools and insights will enable yam breeders to unlock the potential of this staple crop and take full advantage of its adaptability to varied environments.

Acknowledgements

At the University of California, Davis, Genome and Biomedical Sciences facility, we thank Oanh Nguyen for troubleshooting and advice for DNA isolation and PacBio sequencing, Emily Kumimoto for mate-pair libraries, and Lutz Froenicke for management. For facilitating DArTseq genotyping, we thank: Andrzej Kilian (Diversity Arrays Technology); and Clay Sneller, Jackline Chepkoech, Mercy Chepngetich, and IGSS/SEQART staff at BecA-ILRI Hub. We thank the staff of Bioscience Center, Yam Breeding Unit, ...