To monitor genetic diversity in the field it is important that it is measured accurately. Here, we elucidate the potential of single nucleotide polymorphisms (SNPs) for measuring genetic diversity in cassava. The nature and frequency of SNPs was characterised and their utility in genetic diversity assessment compared to that of simple sequence repeats (SSRs). This was achieved by direct sequencing of amplicons in diverse cassava varieties. A total of 26 SNPs were identified from quality sequences of nine genes, giving an estimated frequency of one SNP every 121 nucleotides. Nucleotide diversity ranged from 7.8 × 10−4 to 5.6 × 10−3. Average haplotype-based polymorphic information content (PIC = 0.414) was higher than for individual SNPs (PIC = 0.228). The Mantel test indicated interdependence (r = 0.219; P < 0.001) between SNP and SSR genotypic data. Individual SNPs had lower PIC values than SSRs. For this reason larger numbers of SNPs may be necessary to achieve the same level of discrimination among genotypes provided by SSRs.

Identification, characterisation and application of single nucleotide polymorphisms for diversity assessment in cassava (Manihot esculenta Crantz)

The diploid (2C) amount of DNA in cassava (Manihot esculenta Crantz) is 1.67 picograms (pg) per cell nucleus. This value corresponds to 772 mega-base pairs in the haploid genome. The size of the nuclear genome in cassava is very small in comparison with other Angiosperms. Flow cytometry techniques were used to screen ploidy levels in a large population of in vitro plantlets treated with colchicine and oryzalin (3,5-dinitro-N4,N-dipropylsulphate). Culture of axillary node cuttings for 48 hours in liquid medium supplemented with 2.5 to 5.0 mM colchicine in combination with 2% dimethyl sulfoxide (DMSO) resulted in a high frequency (23 to 42%) of non-chimeric tetraploids in the V3 generation. Although mixoploidy may persist in as many as four cycles of vegetative propagation of node cuttings, solid (non-chimeric) tetraploids can be identified by flow cytometry among in vitro plantlets and then rapidly propagated for field testing. A somatic polyploidization system is proposed for implementation in cassava breeding programmes.

Nuclear DNA content and in vitro induced somatic polyploidization cassava (Manihot esculenta Crantz) breeding

Breeding Bananas and Plantains

With 1 figure

Abstract
To generate a genetic linkage map of cassava (Manihot esculenta Crantz), 58 F1 progenies from a cross between Rayong 90 (female) and Rayong 5 (male) were examined in amplification fragment length polymorphism (AFLP) and simple sequence repeat (SSR) analyses. A total of 469 polymorphic markers consisting of 378 AFLPs generated from 76 primer combinations and 91 SSRs were identified. These markers were analyzed using the joinmap®3.0 package program to construct a genetic linkage map. A total of 33 linkage groups of a common map were constructed from 119 AFLPs and 18 SSRs, spanning 1095 cM with an average of 7.99 cM between markers. The genetic linkage map generated in this study will be useful for genetic studies in cassava particularly for the identification of genetic markers linked to traits of interest, although the complex cassava genome suggests that maybe a long term objective.

Genetic linkage map of cassava (Manihot esculenta Crantz) based on AFLP and SSR markers

The development of the cassava genetic map has promoted research such as the finding of genes associated with the resistance of pests that diminish the production and quality of the crop. Molecular tools, such as markers can facilitate the identification of the genes that dominate resistance to pests this is the specific case of the presence of resistance to the green mite Mononychellus tanajoa (CGM) in cassava (Manihot esculenta). Initially, at International Center for Tropical Agriculture CIAT, individuals populations of backcrosses (BC1), lineage of four denominated families CW, were identified. These BC1 were identified and categorized according to 1-5 scale of damage reported by the Entomology Program at International Center for Tropical Agriculture. Resistant and susceptible individuals were identified. A total of 500 microsatellite markers were evaluated using the bulk segregant analysis (BSA). Five of them expressed polymorphism and showed significant differences between parental and contrast groups and three markers, namely, SSRY 11, SSRY 346 and, NS 1099. Statistical analysis revealed that markers NS 1099 and NS 346 displayed the highest association between resistance and the individuals of families CW 67, CW 66 and CW 67, respectively. On the basis of these results we can recommend the use of microsatellite for further analysis in other populations in order to achieve the of some chromosomal regions conferring resistance to green mite cassava.

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Identificación de microsatélites en yuca asociados con la resistencia al ácaro Mononychellus tanajoa (Acari: Tetranychidae)

Pachytene pairing in relation to pollen fertility was studied in five cultivars of cassava. The two highly pollen fertile clones showed only normal pachytene and later meiotic divisions were also normal. However, in the partially pollen fertile clones different pachytene abnormalities like non-pairing, deletion, duplication and inversion were found in different chromosomes. In C1-1443 as many as five bivalents showed aberrant pachytene pairing. Though there was a slight reduction in chiasma frequency, later divisions were normal. Based on the extent of pachytene abnormalities in different clones, reduction in chiasma frequency, meiotic sequence and normal tapetum development and microsporogenesis, it is concluded that pachytene behaviour had a statutory role in determining the ultimate pollen fertility in cassava.

Pachytene Pairing in Relation to Pollen Fertility in Five Cultivars of Cassava

Seed set and polyembryony in Amorphophallus campanulatus Blume

A completely male sterile clone was identified in the germplasm and detailed meiosis showed it to be asynaptic. At pachytene all the chromosomes remained as univalents without any semblance to pairing. MI aslo showed 36 univalents in 97% of pollen mother cells. The bivalent like association in MI was as low as 0.03 per cell but the absence of pairing at pachytene and the lack of well defined x'mata suggested that they were only univalents lying closely together due to factors other than true pairing. The later stages were not well defined and univalents were noticed to divide. The scattering of chromosomes and irregular groupings resulted in polyads consequently all the pollen were sterile. The type of asynapsis noticed was ‘complete’. The presence of pollen sterility in all the plants of Ce-258 throughout the season ruled out environmental factors and suggested it was of genic nature.

J. S. Jos

Papers

Pachytene Pairing in Relation to Pollen Fertility in Five Cultivars of Cassava

Seed set and polyembryony in Amorphophallus campanulatus Blume

Asynapsis in cassava.