Cassava HapMap: Masking deleterious mutations in a clonal crop species

Ramu, Punna; Esuma, Williams; Kawuki, Robert; Rabbi, Ismail; Egesi, Chiedozie; Jv, Bredeson; Rs, Bart; Verma, J; Es, Buckler; Lü, Fei

doi:10.1101/077123

Cited by 8 publications

(9 citation statements)

References 40 publications

(60 reference statements)

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“…More problematic than the timescale of domestication is the phenomenon that has become known as the cost of domestication (Charlesworth and Willis, 2009;Gepts, 2014;Gaut et al, 2018), that is, the proposal that linked selection can drag deleterious mutants to high frequency (Chun and Fay, 2011;Zhou et al, 2017). Indeed, most crops examined to date contain considerably more deleterious allelic variants than their wild relatives (Renaut and Rieseberg, 2015;Kono et al, 2016;Ramu et al, 2017;Wang et al, 2017;Zhou et al, 2017), with species that are clonally propagated being particularly susceptible to accrue such mutations (Gaut et al, 2018). This phenomenon clearly needs to be carefully considered when planning future agricultural strategies.…”

Section: De Novo Domesticationmentioning

confidence: 99%

De Novo Domestication: An Alternative Route toward New Crops for the Future

2019

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Current global agricultural production must feed over 7 billion people. However, productivity varies greatly across the globe and is under threat from both increased competitions for land and climate change and associated environmental deterioration. Moreover, the increase in human population size and dietary changes are putting an ever greater burden on agriculture. The majority of this burden is met by the cultivation of a very small number of species, largely in locations that differ from their origin of domestication. Recent technological advances have raised the possibility of de novo domestication of wild plants as a viable solution for designing ideal crops while maintaining food security and a more sustainable lowinput agriculture. Here we discuss how the discovery of multiple key domestication genes alongside the development of technologies for accurate manipulation of several target genes simultaneously renders de novo domestication a route toward crops for the future.

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Section: De Novo Domesticationmentioning

confidence: 99%

De Novo Domestication: An Alternative Route toward New Crops for the Future

2019

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“…39 ). Pineapple also had fewer putative selective sweeps than other clonally propagated crops such as cassava, which contains signatures of 224 sweeps 40 . Supplementary Fig.…”

Section: Nature Geneticsmentioning

confidence: 99%

The bracteatus pineapple genome and domestication of clonally propagated crops

et al. 2019

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Merr.) is a fruit crop originated and domesticated in South America. According to Bertoni 2 , the genus name Ananas means 'excellent fruit' in the Guaraní language of Paraguay. Pineapple was domesticated >6,000 years ago with archaeobotanical remains dated 3,500 years ago in South America and distributed to Mesoamerica >2,500 years ago 3-5. Pineapple is clonally propagated using the leafy fruit crown, slips or suckers. Red pineapple (Ananas comosus var. bracteatus) was anciently cultivated for fiber, fruit juice and as a living hedge, and is now a pantropical ornamental 6,7. The bracteatus plant is conspicuous for its bright pink-to-red colored fruit. The name 'bracteatus' refers to its long bracts. The plant is vigorous with long leaves, coarse spines and abundant suckers. Plant fibers have been used in numerous applications that are beneficial to agriculture and the environment, partly

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“…Since several SNPs on the chromosome 4 QTL region are in high LD, no single locus can be 379 highlighted as candidate gene(s) to be associated with CBSD severity ( Figure 4A). The large 380 haplotype on chromosome 4 is an introgression block from the a wild relative of cassava (M. 381 glaziovii) (Jennings, 1959;Bredeson et al, 2016). We further confirmed the presence and 382 segregation of the introgressed genome segment in both panels using a set of diagnostic markers 383 from M. glaziovii ( Figure 4B, supplementary figure 13 and 14).…”

Section: Genome Wide Association Mapping For Cbsv Severity In Cassavamentioning

confidence: 56%

Genome-wide association mapping and genomic prediction unravels CBSD resistance in aManihot esculentabreeding population

Kayondo

Carpio

Lozano

et al. 2017

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13Cassava (Manihot esculenta Crantz), a key carbohydrate dietary source for millions of people in 14 Africa, faces severe yield loses due to two viral diseases: cassava brown streak disease (CBSD) 15 and cassava mosaic disease (CMD). The completion of the cassava genome sequence and the 16 whole genome marker profiling of clones from African breeding programs 17 (www.nextgencassava.org) provides cassava breeders the opportunity to deploy additional 18 breeding strategies and develop superior varieties with both farmer and industry preferred traits. 19Here the identification of genomic segments associated with resistance to CBSD foliar symptoms 20 and root necrosis as measured in two breeding panels at different growth stages and locations is 21 reported. Using genome-wide association mapping and genomic prediction models we describe 22 the genetic architecture for CBSD severity and identify loci strongly associated on chromosomes 23 4 and 11. Moreover, the significantly associated region on chromosome 4 colocalises with a 24Manihot glaziovii introgression segment and the significant SNP markers on chromosome 11 are 25 situated within a cluster of nucleotide-binding site leucine-rich repeat (NBS-LRR) genes 26 previously described in cassava. Overall, predictive accuracy values found in this study varied 27 between CBSD severity traits and across GS models with Random Forest and RKHS showing the 28 highest predictive accuracies for foliar and root CBSD severity scores. 29 30

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Cassava HapMap: Masking deleterious mutations in a clonal crop species

Abstract: Cassava (Manihot esculentaCrantz

Cited by 8 publications

References 40 publications

De Novo Domestication: An Alternative Route toward New Crops for the Future

De Novo Domestication: An Alternative Route toward New Crops for the Future

The bracteatus pineapple genome and domestication of clonally propagated crops

Genome-wide association mapping and genomic prediction unravels CBSD resistance in aManihot esculentabreeding population

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