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

Jessen V. Bredeson; Jessica B. Lyon; Ibukun O. Oniyinde; Nneka R. Okereke; Olufisayo Kolade; Ikenna Nnabue; Christian O. Nwadili; Eva Hřibová; Matthew Parker; Jeremiah Nwogha; Shengqiang Shu; Joseph Carlson; Robert Kariba; Samuel Muthemba; Katarzyna Knop; Geoffrey J. Barton; Anya V. Sherwood; Antonio Lopez-Montes; Robert Asiedu; Ramni Jamnadass; David Goodstein; Chiedozie N. Egesi; Jonathan Featherston; Gordon Simpson; Jaroslav Doležel; Prasad S. Hendre; Allen Van Deynze; Pullikanti Lava Kumar; Jude Ejikeme Obidiegwu; Ranjana Bhattacharjee; Daniel S. Rokhsar

doi:10.1101/2021.04.14.439117

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

Jessen V. Bredeson
, Jessica B. Lyon
, Ibukun O. Oniyinde
, Nneka R. Okereke
, Olufisayo Kolade
, Ikenna Nnabue
, Christian O. Nwadili
, Eva Hřibová
, Matthew Parker
, Jeremiah Nwogha
, Shengqiang Shu
, Joseph Carlson
, Robert Kariba
, Samuel Muthemba
, Katarzyna Knop
, Geoffrey J. Barton
, Anya V. Sherwood
, Antonio Lopez-Montes
, Robert Asiedu
, Ramni Jamnadass

David Goodstein, Chiedozie N. Egesi, Jonathan Featherston, Gordon Simpson, Jaroslav Doležel, Prasad S. Hendre, Allen Van Deynze, Pullikanti Lava Kumar, Jude Ejikeme Obidiegwu (Lead / Corresponding author), Ranjana Bhattacharjee (Lead / Corresponding author), Daniel S. Rokhsar (Lead / Corresponding author)

Research output: Working paper/Preprint › Preprint

Abstract

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 greater yam combined with a dense genetic map derived from African breeding populations. The genome sequence reveals an ancient lineage-specific genome duplication, followed by extensive genome-wide reorganization. Using our new genomic tools we find quantitative trait loci for susceptibility 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.

Original language	English
Place of Publication	Cold Spring Harbor Laboratory
Publisher	BioRxiv
Pages	1-36
Number of pages	36
DOIs	https://doi.org/10.1101/2021.04.14.439117
Publication status	Published - 15 Apr 2021

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10.1101/2021.04.14.439117Licence: CC BY-NC

Chromosome evolution and the genetic basis of agronomically important traits in greater yam
Bredeson, J. (Creator), Lyons, J. (Creator), Oniyinde, I. (Creator), Okereke, N. (Creator), Kolade, O. (Creator), Nnabue, I. (Creator), Okereke, N. (Creator), Nwadili, C. (Creator), Hribova, E. (Creator), Parker, M. (Creator), Nwogha, J. (Creator), Shu, S. (Creator), Carlson, J. (Creator), Kariba, R. (Creator), Muthemba, S. (Creator), Knop, K. (Creator), Barton, G. (Creator), Sherwood, A. (Creator), Lopez-Montes, A. (Creator), Asiedu, R. (Creator), Jamnadass, R. (Creator), Muchugi, A. (Creator), Goodstein, D. (Creator), Egesi, C. (Creator), Featherston, J. (Creator), Asfaw, A. (Creator), Simpson, G. (Creator), Dolezel, J. (Creator), Hendre, P. (Creator), Van Deynze, A. (Creator), Lava Kumar, P. (Creator), Obidiegwu, J. (Creator), Bhattacharjee, R. (Creator) & Rokhsar, D. (Creator), Dryad, 19 Nov 2021
DOI: 10.6078/d1dq54
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Bredeson, J. V., Lyon, 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., ... Rokhsar, D. S. (2021). Chromosome evolution and the genetic basis of agronomically important traits in greater yam. (pp. 1-36). BioRxiv. https://doi.org/10.1101/2021.04.14.439117

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abstract = "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 {\textquotedblleft}orphan crop.{\textquotedblright} Here we address this resource gap by presenting a highly-contiguous chromosome-scale genome assembly of greater yam combined with a dense genetic map derived from African breeding populations. The genome sequence reveals an ancient lineage-specific genome duplication, followed by extensive genome-wide reorganization. Using our new genomic tools we find quantitative trait loci for susceptibility 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.",

author = "Bredeson, \{Jessen V.\} and Lyon, \{Jessica B.\} and Oniyinde, \{Ibukun O.\} and Okereke, \{Nneka R.\} and Olufisayo Kolade and Ikenna Nnabue and Nwadili, \{Christian O.\} and Eva H{\v r}ibov{\'a} and Matthew Parker and Jeremiah Nwogha and Shengqiang Shu and Joseph Carlson and Robert Kariba and Samuel Muthemba and Katarzyna Knop and Barton, \{Geoffrey J.\} and Sherwood, \{Anya V.\} and Antonio Lopez-Montes and Robert Asiedu and Ramni Jamnadass and David Goodstein and Egesi, \{Chiedozie N.\} and Jonathan Featherston and Gordon Simpson and Jaroslav Dole{\v z}el and Hendre, \{Prasad S.\} and \{Van Deynze\}, Allen and Kumar, \{Pullikanti Lava\} and Obidiegwu, \{Jude Ejikeme\} and Ranjana Bhattacharjee and Rokhsar, \{Daniel S.\}",

year = "2021",

month = apr,

day = "15",

doi = "10.1101/2021.04.14.439117",

language = "English",

pages = "1--36",

publisher = "BioRxiv",

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Bredeson, JV, Lyon, JB, Oniyinde, IO, Okereke, NR, Kolade, O, Nnabue, I, Nwadili, CO, Hřibová, E, Parker, M, Nwogha, J, Shu, S, Carlson, J, Kariba, R, Muthemba, S, Knop, K, Barton, GJ, Sherwood, AV, Lopez-Montes, A, Asiedu, R, Jamnadass, R, Goodstein, D, Egesi, CN, Featherston, J, Simpson, G, Doležel, J, Hendre, PS, Van Deynze, A, Kumar, PL, Obidiegwu, JE, Bhattacharjee, R & Rokhsar, DS 2021 'Chromosome evolution and the genetic basis of agronomically important traits in greater yam' BioRxiv, Cold Spring Harbor Laboratory, pp. 1-36. https://doi.org/10.1101/2021.04.14.439117

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AU - Bredeson, Jessen V.

AU - Lyon, Jessica B.

AU - Oniyinde, Ibukun O.

AU - Okereke, Nneka R.

AU - Kolade, Olufisayo

AU - Nnabue, Ikenna

AU - Nwadili, Christian O.

AU - Hřibová, Eva

AU - Parker, Matthew

AU - Nwogha, Jeremiah

AU - Shu, Shengqiang

AU - Carlson, Joseph

AU - Kariba, Robert

AU - Muthemba, Samuel

AU - Knop, Katarzyna

AU - Barton, Geoffrey J.

AU - Sherwood, Anya V.

AU - Lopez-Montes, Antonio

AU - Asiedu, Robert

AU - Jamnadass, Ramni

AU - Goodstein, David

AU - Egesi, Chiedozie N.

AU - Featherston, Jonathan

AU - Simpson, Gordon

AU - Doležel, Jaroslav

AU - Hendre, Prasad S.

AU - Van Deynze, Allen

AU - Kumar, Pullikanti Lava

AU - Obidiegwu, Jude Ejikeme

AU - Bhattacharjee, Ranjana

AU - Rokhsar, Daniel S.

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N2 - 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 greater yam combined with a dense genetic map derived from African breeding populations. The genome sequence reveals an ancient lineage-specific genome duplication, followed by extensive genome-wide reorganization. Using our new genomic tools we find quantitative trait loci for susceptibility 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.

AB - 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 greater yam combined with a dense genetic map derived from African breeding populations. The genome sequence reveals an ancient lineage-specific genome duplication, followed by extensive genome-wide reorganization. Using our new genomic tools we find quantitative trait loci for susceptibility 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.

U2 - 10.1101/2021.04.14.439117

DO - 10.1101/2021.04.14.439117

M3 - Preprint

SP - 1

EP - 36

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

PB - BioRxiv

CY - Cold Spring Harbor Laboratory

ER -

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

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

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