Orphan legume crops enter the genomics era!

Varshney, Rajeev K.; Close, Timothy J.; Singh, Nagendra; Hoisington, David; Cook, Douglas R.

doi:10.1016/j.pbi.2008.12.004

Cited by 229 publications

(195 citation statements)

References 44 publications

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“…Among the various molecular markers, microsatellites or simple sequence repeats (SSR) have shown to be very useful, because these markers showed high polymorphism, reproducible and easy to handle (Varshney et al 2005(Varshney et al , 2009Datta et al 2011). Though in lentil, a number of SSR markers have been developed (Hamwieh et al 2005;Kaur et al 2011;Datta et al 2011), availability of polymorphic SSR markers and their use in analysis of the genetic diversity is still limited in lentil compared to other pulses such as chickpea (Hamwieh et al 2005(Hamwieh et al , 2009Kaur et al 2011;Datta et al 2011).…”

Section: Introductionmentioning

confidence: 99%

Diversification of indigenous gene- pool by using exotic germplasm in lentil (Lens culinaris Medikus subsp. culinaris)

Kumar

Srivastva

Singh

et al. 2013

Physiol Mol Biol Plants

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Genetic diversity was studied among 21 accessions of lentil using SSR markers and morphological traits in order to assess the diversification of Indian gene-pool of lentil through introgression of exotic genes and introduction of germplasm. Among these , 16 genotypes either had 'Precoz' gene, an Argentine line in their pedigree or genes from introduced lines from ICARDA. Sixty five SSR markers and eight phenotypic traits were used to analyse the level of genetic diversity in these genotypes. Forty three SSR markers (66 %) were polymorphic and generated a total of 177 alleles with an average of 4.1 alleles per SSR marker. Alleles per marker ranged from 2 to 6. The polymorphic information content ranged 0.33 to 0.80 with an average of 0.57, suggesting that SSR markers are highly polymorphic among the studied genotypes. Genetic dissimilarity based a dendrogram grouped these accessions into two main clusters (cluster I and cluster II) and it ranged 33 % to 71 %, suggesting high level of genetic diversity among the genotypes. First three components of PCA based morphological traits explained higher variance (95.6 %) compared to PCA components based on SSR markers (42.7 %) of total genetic variance. Thus, more diversity was observed for morphological traits and genotypes in each cluster and sub-cluster showed a range of variability for seed size, earliness, pods/plant and plant height. Molecular and phenotypic diversity analysis thus suggested that use of germplasm of exotic lines have diversified the genetic base of lentil germplasm in India. This diversified gene-pool will be very useful in the development of improved varieties of lentil in order to address the effect of climate change, to adapt in new cropping systems niches such as mixed cropping, relay cropping, etc. and to meet consumers' preference.

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Section: Introductionmentioning

confidence: 99%

Diversification of indigenous gene- pool by using exotic germplasm in lentil (Lens culinaris Medikus subsp. culinaris)

Kumar

Srivastva

Singh

et al. 2013

Physiol Mol Biol Plants

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“…One of the reasons for slow progress in the molecular breeding of the important legume crop like pigeon pea has been attributed to the limited availability of molecular markers and non-availability of any linkage map so far. Although, tremendous progress has been made in terms of availability of genomic resources in this orphan legume crop in recent times (Varshney et al 2009(Varshney et al , 2010, availability of a framework linkage map was lacking. In the present study, we report the first framework linkage map of pigeon pea based on an interspecific F 2 mapping population using DArT markers.…”

Section: Discussionmentioning

confidence: 99%

The first genetic map of pigeon pea based on diversity arrays technology (DArT) markers

Shi

Saxena

Kulwal

et al. 2011

J Genet

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With an objective to develop a genetic map in pigeon pea (Cajanus spp.), a total of 554 diversity arrays technology (DArT) markers showed polymorphism in a pigeon pea F 2 mapping population of 72 progenies derived from an interspecific cross of ICP 28 (Cajanus cajan) and ICPW 94 (Cajanus scarabaeoides). Approximately 13% of markers did not conform to expected segregation ratio. The total number of DArT marker loci segregating in Mendelian manner was 405 with 73.1% (P > 0.001) of DArT markers having unique segregation patterns. Two groups of genetic maps were generated using DArT markers. While the maternal genetic linkage map had 122 unique DArT maternal marker loci, the paternal genetic linkage map has a total of 172 unique DArT paternal marker loci. The length of these two maps covered 270.0 cM and 451.6 cM, respectively. These are the first genetic linkage maps developed for pigeon pea, and this is the first report of genetic mapping in any grain legume using diversity arrays technology.[Yang S. Y., Saxena R. K., Kulwal P. L., Ash G. J., Dubey A., Harper J. D. I., Upadhyaya H. D., Gothalwal R., Kilian A. and Varshney R. K. 2011 The first genetic map of pigeon pea based on diversity arrays technology (DArT) markers. J. Genet. 90, [103][104][105][106][107][108][109]

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“…Rapid advances in genomic technologies will facilitate the domestication of species such as marama bean and African locust bean [173]. Both species have been targeted for genome sequencing in the African Orphan Crops Consortium (http://africanorphancrops.org/).…”

Section: African Locust Beanmentioning

confidence: 99%

The Impact of Genetic Changes during Crop Domestication

et al. 2018

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Abstract:Humans have domesticated hundreds of plant and animal species as sources of food, fiber, forage, and tools over the past 12,000 years, with manifold effects on both human society and the genetic structure of the domesticated species. The outcomes of crop domestication were shaped by selection driven by human preferences, cultivation practices, and agricultural environments, as well as other population genetic processes flowing from the ensuing reduction in effective population size. It is obvious that any selection imposes a reduction of diversity, favoring preferred genotypes, such as nonshattering seeds or increased palatability. Furthermore, agricultural practices greatly reduced effective population sizes of crops, allowing genetic drift to alter genotype frequencies. Current advances in molecular technologies, particularly of genome sequencing, provide evidence of human selection acting on numerous loci during and after crop domestication. Population-level molecular analyses also enable us to clarify the demographic histories of the domestication process itself, which, together with expanded archaeological studies, can illuminate the origins of crops. Domesticated plant species are found in 160 taxonomic families. Approximately 2500 species have undergone some degree of domestication, and 250 species are considered to be fully domesticated. The evolutionary trajectory from wild to crop species is a complex process. Archaeological records suggest that there was a period of predomestication cultivation while humans first began the deliberate planting of wild stands that had favorable traits. Later, crops likely diversified as they were grown in new areas, sometimes beyond the climatic niche of their wild relatives. However, the speed and level of human intentionality during domestication remains a topic of active discussion. These processes led to the so-called domestication syndrome, that is, a group of traits that can arise through human preferences for ease of harvest and growth advantages under human propagation. These traits included reduced dispersal ability of seeds and fruits, changes to plant structure, and changes to plant defensive characteristics and palatability. Domestication implies the action of selective sweeps on standing genetic variation, as well as new genetic variation introduced via mutation or introgression. Furthermore, genetic bottlenecks during domestication or during founding events as crops moved away from their centers of origin may have further altered gene pools. To date, a few hundred genes and loci have been identified by classical genetic and association mapping as targets of domestication and postdomestication divergence. However, only a few of these have been characterized, and for even fewer is the role of the wild-type allele in natural populations understood. After domestication, only favorable haplotypes are retained around selected genes, which creates a genetic valley with extremely low genetic diversity. These "selective sweeps" can allow mildly deleterious...

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Orphan legume crops enter the genomics era!

Cited by 229 publications

References 44 publications

Diversification of indigenous gene- pool by using exotic germplasm in lentil (Lens culinaris Medikus subsp. culinaris)

Diversification of indigenous gene- pool by using exotic germplasm in lentil (Lens culinaris Medikus subsp. culinaris)

The first genetic map of pigeon pea based on diversity arrays technology (DArT) markers

The Impact of Genetic Changes during Crop Domestication

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