Key message
Consolidates relevant molecular and phenotypic information on cassava to demonstrate relevance of heterosis, and alternatives to exploit it by integrating different tools. Ideas are useful to other asexually reproduced crops.

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Conventional breeding, marker-assisted selection, genomic selection and inbreeding in clonally propagated crops: a case study for cassava.

Pearl millet is an important component of food security in the semi-arid tropics and is assuming greater importance in the context of changing climate and increasing demand for highly nutritious food and feed. Molecular tools have been developed and applied for pearl millet on a limited scale. However, the existing tool kit needs to be strengthened further for its routine use in applied breeding programs. Here, we report enrichment of the pearl millet molecular linkage map by exploiting low-cost and high-throughput Diversity Arrays Technology (DArT) markers. Genomic representation from 95 diverse genotypes was used to develop a DArT array with circa 7,000 clones following PstI/BanII complexity reduction. This array was used to genotype a set of 24 diverse pearl millet inbreds and 574 polymorphic DArT markers were identified. The genetic relationships among the inbred lines as revealed by DArT genotyping were in complete agreement with the available pedigree data. Further, a mapping population of 140 F7 Recombinant Inbred Lines (RILs) from cross H 77/833-2 × PRLT 2/89-33 was genotyped and an improved linkage map was constructed by integrating DArT and SSR marker data. This map contains 321 loci (258 DArTs and 63 SSRs) and spans 1148 cM with an average adjacent-marker interval length of 3.7 cM. The length of individual linkage groups (LGs) ranged from 78 cM (LG 3) to 370 cM (LG 2). This better-saturated map provides improved genome coverage and will be useful for genetic analyses of important quantitative traits. This DArT platform will also permit cost-effective background selection in marker-assisted backcrossing programs as well as facilitate comparative genomics and genome organization studies once DNA sequences of polymorphic DArT clones are available.

/pdf/development-of-a-molecular-linkage-map-of-pearl-millet-5eel6a7uj7.pdf

Development of a molecular linkage map of pearl millet integrating DArT and SSR markers

Empirical evaluation of DArT, SNP, and SSR marker-systems for genotyping, clustering, and assigning sugar beet hybrid varieties into populations

New Approaches to Cassava Breeding

Background
Numerous rye accessions are stored in ex situ genebanks worldwide. Little is known about the extent of genetic diversity contained in any of them and its relation to contemporary varieties, since to date rye genetic diversity studies had a very limited scope, analyzing few loci and/ or few accessions. Development of high throughput genotyping methods for rye opened the possibility for genome wide characterizations of large accessions sets. In this study we used 1054 Diversity Array Technology (DArT) markers with defined chromosomal location to characterize genetic diversity and population structure in a collection of 379 rye accessions including wild species, landraces, cultivated materials, historical and contemporary rye varieties.

/pdf/genome-wide-characterization-of-genetic-diversity-and-sfwzoejlzw.pdf

Genome-wide characterization of genetic diversity and population structure in Secale

Several molecular marker systems have been developed for assessing genetic diversity in crop germplasm collections. A trade-off often exists between the number of loci that can feasibly be sampled by a marker system and the amount of information provided by each locus. We com­ pared the usefulness of two marker systems for revealing genetic diversity and population structure in cassava (~fanihot esculenta Crantz): simple sequence repeats (SSRs) and diversity array technology (DArT) markers. DArTs survey many more loci per reaction than do SSRs; however, as bi-allelic, dominant markers, DArTs provide less polymorphism information per locus. Genetic differentiation was assessed in a randomly selected set of 436 cassava acces­ sions, consisting of 155 African and 281 Latin American accessions. A genome-wide set of 36 SSR markers and a DArT array of approximately 1000 polymorphic clones were used to assess genetic diversity and differentiation. Cluster analyses were performed using principal coordinate analysis (PCoA). Results were compared with a priori expectations of genetic differentiation based on previous genetic analyses. Analyses of the two datasets generated broadly similar clustering patterns. However, SSRs revealed greater differentiation than DArTs, and more effectively recovered patterns of genetic differentiation observed in previous analyses (differentiation between Latin American and African accessions, and some geogra­ phical differentiation within each of these groups). These results suggest that SSR markers, while low throughput in comparison with DArTs, are relatively better at detecting genetic differentiation in cassava germ plasm collections. Nonetheless, DArTs will likely prove useful in 'orphan crop' species, where alternative molecular markers have not been developed.

Comparison of simple sequence repeat (SSR) and diversity array technology (DArT) markers for assessing genetic diversity in cassava Manihot esculenta Crantz)

M. Adeleke

Papers

Comparison of simple sequence repeat (SSR) and diversity array technology (DArT) markers for assessing genetic diversity in cassava Manihot esculenta Crantz)