Yield gains and associated changes in an early yellow bi-parental maize population following genomic selection for Striga resistance and drought tolerance.

BACKGROUND: Maize yield potential is rarely maximized in sub-Saharan Africa (SSA) due to the devastating effects of drought stress and Striga hermonthica parasitism. This study was conducted to determine the gains in grain yield and associated changes in an early-maturing yellow bi-parental maize population (TZEI 17 x TZEI 11) F3 following genomic selection (GS) for improved grain yield, Striga resistance and drought tolerance. Fifty S1 lines were extracted from each of cycles C0, C1, C2 and C3 of the population and crossed to a tester TZEI 23 to generate 200 testcrosses. The testcrosses were evaluated under drought, artificial Striga-infested and optimal (free from Striga infestation and without limitation of water and nitrogen) environments in Nigeria, 2014-2017. RESULTS: Gains in grain yield of 498 kg ha- 1 cycle- 1 (16.9% cycle- 1) and 522 kg ha- 1 cycle- 1 (12.6% cycle- 1) were obtained under Striga-infested and optimal environments, respectively. The yield gain under Striga-infested environments was associated with increased plant and ear heights as well as improvement in root lodging resistance, husk cover, ear aspect and Striga tolerance. Under optimal environments, yield gain was accompanied by increase in plant and ear heights along with improvement of husk cover and ear rot resistance. In contrast, genomic selection did not improve grain yield under drought but resulted in delayed flowering, poor pollen-silk synchrony during flowering and increased ear height. Genetic variances and heritabilities for most measured traits were not significant for the selection cycles under the research environments. Ear aspect was a major contributor to grain yield under all research environments and could serve as an indirect selection criterion for simultaneous improvement of grain yield under drought, Striga and optimal environments. CONCLUSION: This study demonstrated that genomic selection was effective for yield improvement in the bi-parental maize population under Striga-infested environments and resulted in concomitant yield gains under optimal environments. However, due to low genetic variability of most traits in the population, progress from further genomic selection could only be guaranteed if new sources of genes for Striga resistance and drought tolerance are introgressed into the population.

Genetic Variances and Heritabilities of Traits of an Early Yellow Maize Population after Cycles of Improvement for Striga Resistance and Drought Tolerance.

Drought and Striga are principal constraints to maize (Zea mays L.) production in sub-Saharan Africa. An early yellow maize population, TZE-Y Pop DT STR, which had undergone five cycles of selection for resistance to Striga, followed by three cycles of improvement for drought tolerance, was investigated for yield gains, changes in genetic variance, and interrelationships among traits under drought stress and optimum environments. Two hundred and forty S1 lines comprising 60 each from the base population and subsequent populations from three selection cycles improved for grain yield and drought tolerance were assessed under drought and optimal environments in Nigeria from 2010 to 2012. Genetic improvements in grain yield of 423 and 518 kg ha-1 cycle-1 were achieved under drought stress and optimal environments. Predicted improvements in selection for yield were 348 and 377 kg ha-1 cycle-1 under drought stress and optimum environments, respectively. The highest yield observed in C3 was accompanied by reduced days to silking and anthesis-silking interval, improved plant aspect and ear aspect, and increased plant height and ears per plant across research environments, as well as improved stay-green characteristic under drought. The level of genetic variability for yield and a few other traits were maintained under drought and optimal environments in the population. The presence of residual genetic variability for yield and other assayed traits in C3 indicated that progress could be made from future selection in the population depending on the ability of breeders to identify outstanding genotypes and the precision level of experimentation. Substantial improvement has been made in yield and drought tolerance in C3 of the population.

Gains in Grain Yield of Extra-Early Maize during Three Breeding Periods under Drought and Rainfed Conditions.

Drought is a key maize (Zea mays L.) production constraint in sub-Saharan Africa. Fourteen, fifteen, and twenty-five extra-early maturing maize cultivars, with varying Striga resistance and drought and low soil N tolerance, were developed from 1995 to 2000 (Period 1), 2001 to 2006 (Period 2), and 2007 to 2012 (Period 3), respectively. The objectives of this study were to examine yield gains in the cultivars and to investigate inter-trait relationships and yield stability under six drought and 17 rainfed conditions in West Africa from 2013 to 2016. Annual rate of yield increase across cultivars was 0.034 (3.28%) and 0.068 Mg ha-1 (2.25%), whereas yield gains per period were 0.17 and 0.38 Mg ha-1 under drought and rainfed environments, respectively. Yield gains under drought and rainfed environments were related to prolonged flowering period, increased plant and ear heights, improved stalk lodging, and ear and plant aspects, whereas delayed leaf senescence and increased number of ears per plant accompanied yield improvement under drought only. Ear aspect and number of ears per plant were primary contributors to yield and could be used as selection criteria for yield enhancement under drought and rainfed conditions. High-yielding and stable cultivars across all environments based on additive main effects and multiplicative interaction (AMMI) biplot included '2004 TZEE-Y Pop STR C4' and 'TZEE-W Pop STR BC2 C0' of Period 2 and '2009 TZEE-W STR', 'TZEE-Y STR 106', 'TZEE-W STR 107', and 'TZEE-W DT C0 STR C5' of Period 3. These cultivars could be commercialized to improve food self-sufficiency in sub-Saharan Africa.

Sequence diversity among badnavirus isolates infecting yam (Dioscorea spp.) in Ghana, Togo, Benin and Nigeria.

We analysed the sequence diversity in the reverse transcriptase (RT)/ribonuclease H (RNaseH) coding region of 19 badnavirus isolates infecting yam (Dioscorea spp.) in Ghana, Togo, Benin, and Nigeria. Phylogenetic analysis of the deduced amino acid sequences revealed that the isolates are broadly divided into two distinct species, each clustering with Dioscorea alata bacilliform virus (DaBV) and Dioscorea sansibarensis bacilliform virus (DsBV). Fourteen isolates had 90-96% amino acid identity with DaBV, while four isolates had 83-84% amino acid identity with DsBV. One isolate from Benin, BN4Dr, was distinct and had 77 and 75% amino acid identity with DaBV and DsBV, respectively, and may be a member of a new badnavirus species infecting yam in West Africa. Viruses of the two main species were present in Ghana, Togo and Benin and were observed to infect both D. alata and D. rotundata indiscriminately. This is the first confirmed report of DsBV infection in yam in Ghana and Togo. The results of this study demonstrate that members of two distinct species of badnaviruses infect yam in the West African yam zone and suggest a putative new species, BN4Dr. We also conclude that these species are not confined to limited geographic regions or specific for yam host species. However, the three badnavirus species are serologically related. The sequence information obtained from this study can be used to develop PCR-based diagnostics to detect members of the various species and/or strains of badnaviruses infecting yam in West Africa.

First Report of Cucumber mosaic virus in Yams (Dioscorea spp.) in Ghana, Togo, and Republic of Benin in West Africa.

Yam (Dioscorea spp., family Dioscoreaceae) is one of the most important food crops cultivated in the West African yam zone comprising the forest and savannah areas of Nigeria, Ghana, Côte d'Ivoire, Republic of Benin, and Togo, which account for more than 90% of the 4.59 million ha of yam cultivation worldwide (1). A survey was conducted in 2005 to document viruses in yams in Ghana, Togo, and the Republic of Benin. Samples (1,405) from five species of yam showing mosaic, chlorosis, and stunting as well as asymptomatic plants were tested for Dioscorea bacilliform virus (DBV, genus Badnavirus), Yam mosaic virus (YMV, genus Potyvirus), and Yam mild mosaic virus (YMMV, genus Potyvirus), the three most common viruses infecting yams. In addition, samples were tested for Cucumber mosaic virus (CMV), since CMV was previously reported to infect yams in Côte d'Ivoire (2) and Nigeria (3). In protein-A sandwich-ELISA with polyclonal antibodies to a cowpea isolate of CMV, 23 of the 1,405 samples (6 of 218 samples from Togo, 13 of 628 samples from Ghana, and 4 of 559 samples from Republic of Benin) tested positive for CMV. The CMV-positive samples were from D. alata (N = 16) and D. rotundata (N = 7), whereas all samples from D. cayenensis, D. dumetorum, and D. bulbifera tested negative. CMV was detected as mixed infections with DBV, YMV, or YMMV in 21 of 23 samples. Some of these samples showed puckering, chlorosis, mottling, and crinkling, whereas some plants infected by two or more viruses were asymptomatic. Only two samples from D. rotundata had a single infection of CMV and they showed mild chlorotic symptoms in young leaves that were inconspicuous in mature leaves. In sap inoculations, the virus induced systemic mosaic in Nicotiana glutinosa. The presence of CMV in ELISA-positive yam samples was further confirmed by immunocapture-reverse transcription (IC-RT)-PCR using CMV antibodies as trapping antibody and oligonucleotide primers specific for a 485 nt corresponding to 3' end of the coat protein gene and C-terminal noncoding region of RNA-3 (4). To confirm the specificity of IC-RT-PCR, the 485-bp amplicons from an isolate from the Republic of Benin was cloned into pCR2.1 (Invitrogen, Carlsbad, CA) and three independent clones were sequenced from both orientations. Pairwise comparison of a consensus sequence (Accession No. EU274471) with corresponding sequences of other CMV isolates deposited in GenBank showed 99% identity at the nucleotide sequence level (Accession No. U22821) and revealed that the CMV isolate from yam belongs to sub-Group IA. To our knowledge, this is the first report of CMV infection in yams (D. alata and D. rotundata) in Ghana, Togo, and the Republic of Benin. Together with a previous documentation of CMV in D. alata and D. trifida in Côte d'Ivoire and Nigeria (2,3), this report adds to existing knowledge on distribution of CMV in yams with implications for yam production and germplasm distribution in the West Africa Region. References: (1) FAO. Online publication. FAOSTAT, 2007. (2) C. Fauquet and J. C. Thouvenel. Plant Viral Diseases in the Ivory Coast. ORSTROM: Documentation Techniques. Paris, 1987. (3) Jd'A. Hughes et al. Phytopathology 87:S45, 1997. (4) S. Wylie et al. Aus. J. Agric. Res. 44:41, 1993.

Phases of dormancy in Yam tubers (Dioscorea rotundata).

BACKGROUND AND AIMS: The control of dormancy in yam (Disocorea spp.) tubers is poorly understood and attempts to shorten the long dormant period (i.e. cause tubers to sprout or germinate much earlier) have been unsuccessful. The aim of this study was to identify and define the phases of dormancy in Dioscorea rotundata tubers, and to produce a framework within which dormancy can be more effectively studied. METHODS: Plants of 'TDr 131' derived from tissue culture were grown in a glasshouse simulating temperature and photoperiod at Ibadan (7 degrees N), Nigeria to produce tubers. Tubers were sampled on four occasions: 30 d before shoot senescence (149 days after planting, DAP), at shoot senescence (179 DAP), and twice during storage at a constant 25 degrees C (269 and 326 DAP). The development of the apical shoot bud was described from tissue sections. In addition, the responsiveness of shoot apical bud development to plant growth regulators (gibberellic acid, 2-chloroethanol and thiourea) applied to excised tuber sections was also examined 6 and 12 d after treatment. KEY RESULTS AND CONCLUSIONS: Three phases of tuber dormancy are proposed: Phase I, from tuber initiation to the appearance of the tuber germinating meristem; Phase II, from the tuber germinating meristem to initiation of foliar primordium; and Phase III, from foliar primordium to appearance of the shoot bud on the surface of the tuber. Phase I is the longest phase (approx. 220 d in 'TDr 131'), is not affected by PGRs and is proposed to be an endo-dormant phase. Phases II and III are shorter (<70 d in total), are influenced by PGRs and environmental conditions, and are therefore endo-/eco-dormant phases. To manipulate dormancy to allow off-season planting and more than one generation per year requires that the duration of Phase I is shortened.

In vitro, greenhouse and field assessments of cassava lines for resistance to anthracnose disease caused by Colletotrichum gloeosporioides f.sp. manihotis.

Fifty-three cassava lines were selected from breeding populations at the International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria and screened in vitro for resistance to cassava anthracnose disease (CAD). The in vitro inoculation of stem cuttings with the fungus Colletotrichum gloeosporioides f.sp. manihotis showed significant differences (p +/- 0.05) in acervuli production and in the sensitivity of the cassava lines to the fungal infection after 7 days of incubation at 25 degrees C. Cassava lines 88/01084, 91/00595, 91/00475, 91/00344, 91/00684, 91/00313, 91/00422, and 91/00344 were highly resistant, with necrotic lesion sizes less than 7 mm. In contrast pedigree lines 88/02549, 89/0008, 91/00390 and 91/00402 were highly susceptible with the largest necrotic lesion size being greater than 20 mm. Ten cassava lines from the in vitro screening that showed varying levels of resistance to CAD were selected, based on their flowering abilities for diallel hydridization trials, and were further screened in greenhouse and field trials for CAD resistance. The greenhouse and field screening showed significant varietal differences (p +/- 0.05) in sensitivity to the fungus. In all cases, the progeny lines showed correlated levels of resistance irrespective of the type of screening or assessments. Correlation analysis of the in vitro, greenhouse and field assessments showed that there was a good correspondence among all three methods of evaluating for CAD.

A genetic linkage map of Guinea yam ( Dioscorea rotundata Poir.) based on AFLP markers.

A genetic linkage map of the tetraploid white yam ( Dioscorea rotundata Poir.) was constructed based on 341 co-dominantly scored amplified fragment length polymorphism (AFLP) markers segregating in an intraspecific F(1) cross. The F(1) mapping population was produced by crossing a landrace cultivar TDr 93-1 as female parent to a breeding line TDr 87/00211 as the male parent. The marker segregation data were split into maternal and paternal data sets, and separate genetic linkage maps were constructed since the mapping population was an F(1) cross between two presumed heterozygous parents. The markers segregated like a diploid cross-pollinator population suggesting that the D. rotundata genome is an allo-tetraploid (2n = 4 x = 40). The maternal map comprised 155 markers mapped on 12 linkage groups with a total map length of 891 cM. Three linkage groups consisted of maternal parent markers only. The paternal map consisted of 157 markers mapped on 13 linkage groups with a total map length of 852 cM. Three and one quantitative trait loci (QTLs) with effects on resistance to Yam Mosaic Virus (YMV) were identified on the maternal and paternal linkage maps, respectively. Prospects for detecting more QTLs and using marker-assisted selection in white yam breeding appear good, but this is subject to the identification of additional molecular markers to cover more of the genome.

A genetic linkage map of water yam ( Dioscorea alata L.) based on AFLP markers and QTL analysis for anthracnose resistance.

A genetic linkage map of the tetraploid water yam ( Dioscorea alata L.) genome was constructed based on 469 co-dominantly scored amplified fragment length polymorphism (AFLP) markers segregating in an intraspecific F(1) cross. The F(1) was obtained by crossing two improved breeding lines, TDa 95/00328 as female parent and TDa 87/01091 as male parent. Since the mapping population was an F(1) cross between presumed heterozygous parents, marker segregation data from both parents were initially split into maternal and paternal data sets, and separate genetic linkage maps were constructed. Later, data analysis showed that this was not necessary and thus the combined markers from both parents were used to construct a genetic linkage map. The 469 markers were mapped on 20 linkage groups with a total map length of 1,233 cM and a mean marker spacing of 2.62 cM. The markers segregated like a diploid cross-pollinator population suggesting that the water yam genome is allo-tetraploid (2n = 4 x = 40). QTL mapping revealed one AFLP marker E-14/M52-307 located on linkage group 2 that was associated with anthracnose resistance, explaining 10% of the total phenotypic variance. This map covers 65% of the yam genome and is the first linkage map reported for D. alata. The map provides a tool for further genetic analysis of traits of agronomic importance and for using marker-assisted selection in D. alata breeding programmes. QTL mapping opens new avenues for accumulating anthracnose resistance genes in preferred D. alata cultivars.

First Report of Nattrassia mangiferae as a Postharvest Fungal Pathogen of White Yam (Dioscorea rotundata) in Nigeria.

A survey of the yam growing areas of Nigeria was conducted in January 1999 to identify the major fungal pathogens responsible for considerable tuber rot losses in storage. A total of 150 tubers of white yam showing rot symptoms were collected from 30 barns at 18 locations spanning three agroecologies (guinea savanna, forest/savanna transition, and forest) within the yam belt of Nigeria. Tuber pieces were cut at the interface between healthy and infected tissue, surface-sterilized in 10% bleach solution (0.05% sodium hypochlorite), rinsed in sterile distilled water, and plated on potato dextrose agar (PDA; Difco Laboratories, Detroit, MI) amended with lactic acid (1ml/liter) to reduce bacterial contamination. Cultures were incubated at 28°C for 4 days. Isolations from the guinea savanna agroecology showed that Nattrassia mangiferae Sutton & Dyko (synonym Hendersonula toruloidea) (3) had 42% frequency of occurence, Botryodiplodia theobromae Pat. (10%), Penicillium oxalicum Curie & Thom. (12%), and Aspergillus niger Tiegh. had 50% frequency of occurrence of the total fungi isolated from this region. In the forest/savanna transition agroecology, N. mangiferae had 28% frequency of occurrence, while B. theobromae, P. oxalicum, and A. niger had 10, 14, and 50% frequency of occurrence, respectively. In the forest agroecology, N. mangiferae and B. theobromae had 6% frequency of occurrence, while P. oxalicum and A. niger had 17 and 72% frequency of occurrence, respectively. N. mangiferae was more frequent in occurrence than the two known major fungal pathogens (B. theobromae and P. oxalicum) of yam tuber in storage. Hence, its pathogenicity was tested on healthy tubers. Fifteen healthy tubers were wounded and inoculated individually with 7-day-old mycelial plugs of each of 10 isolates of N. mangiferae from each agroecology using the cork borer technique (2), placed in polythene bags, and stored in a barn for 14 days at 27± 2°C. Control tubers were inoculated with sterile agar plugs. Tubers were sliced at the points of inoculation, and lesion development was measured. N. mangiferae was found to be pathogenic in yam tubers causing soft, wet, brown rots similar to those observed in natural infections, and it appeared as dark necrotic lesions on tuber surface. In culture however, colonies are fluffy with olivaceous gray coloration that gradually darkens as the fungus matures. The fungus grows rapidly on PDA and is able to attain a radial diameter of 90 mm by the fourth day after inoculation. Cultures reisolated from the inoculated tubers matched those used for inoculation. Isolates obtained from the forest/savanna transition agroecology caused significantly (P < 0.05) larger rot lesions (24.67mm) than those obtained from the guinea savanna (18.33mm), and the forest (21.67mm). In another experiment, tubers were inoculated with N. mangiferae without wounding the tubers (mycelial disks were firmly placed on the tuber surface to make adequate contact), and the control tubers were inoculated with sterile agar plugs. Tubers inoculated without wounding remained asymptomatic when assessed for rot development. N. mangiferae has been reported as a root and stem rot pathogen of cassava in West Africa (1). To our knowledge, this is the first report of N. mangiferae causing tuber rot of yams in storage. References: (1) W. Msikita et al. Plant Dis. 81:1332, 1997. (2) N. Okafor Exp. Agric. 2:179, 1966. (3) B. C. Sutton and B. J. Dyko. Mycol. Res. 93:466, 1989.

Variability of chloroplast DNA and nuclear ribosomal DNA in cassava (Manihot esculenta Crantz) and its wild relatives.

Chloroplast DNA (cp) and nuclear ribosomal DNA (rDNA) variation was investigated in 45 accessions of cultivated and wild Manihot species. Ten independent mutations, 8 point mutations and 2 length mutations were identified, using eight restriction enzymes and 12 heterologous cpDNA probes from mungbean. Restriction fragment length polymorphism analysis defined nine distinct chloroplast types, three of which were found among the cultivated accessions and six among the wild species. Cladistic analysis of the cpDNA data using parsimony yielded a hypothetical phylogeny of lineages among the cpDNAs of cassava and its wild relatives that is congruent with morphological evolutionary differentiation in the genus. The results of our survey of cpDNA, together with rDNA restriction site change at the intergenic spacer region and rDNA repeat unit length variation (using rDNA cloned fragments from taro as probe), suggest that cassava might have arisen from the domestication of wild tuberous accessions of some Manihot species, followed by intensive selection. M. esculenta subspp flabellifolia is probably a wild progenitor. Introgressive hybridization with wild forms and pressures to adapt to the widely varying climates and topography in which cassava is found might have enhanced the crop's present day variability.

Resistance toHeterodera avenue in the rye genome of triticale.

The cereal cyst nematode,Heterodera avenue Wollenweber, is a serious pest of cereals in many countries. A high level of resistance to the unique Australian pathotype of the nematode has been demonstrated in a triticale line (T701-4-6), which was originally obtained from CIMMYT. The level of resistance is similar to that in rye cultivar, South Australian, but higher than that in the wheat line (AUS 10894), hitherto reported to have useful resistance to the Australian pathotype. The gene for resistance was located on rye chromosome 6 (6R) after backcrossing the T701-4-6 line to wheat and correlating the resistance with the presence of individual rye chromosomes identified by morphological, cytological, and isozyme markers. Preliminary evidence suggests that the gene is located on the long arm of6R. To transfer the resistance to wheat, double monosomics of6R and6D in aph1bph1b homozygous background were selected from F2 progeny from a cross of disomic6R substitution for6D to theph1b mutant. Selfed seeds from these F2 plants will be screened for wheat-rye chromosome recombinants.

Tetraploids, triploids, and 2n pollen from diploid interspecific crosses with cassava.

Interspecific crosses of five cultivated cassava varieties (2n=36) were made with two related Manihot species, M. epruinosa (2n=36) and M. glaziovii (2n=36). From these diploid interspecific crosses, four spontaneous tetraploids (2n=4x=72) and two triploids (2n=3x=54) were isolated for the first time in cassava. Occurrence of relatively high frequencies (0.1%-35.6%) of 2n pollen and of apomixis seems to be associated with sexual polyploidization. The tetraploids and triploids were very vigorous and one of the tetraploids performed as well as the best variety in uniform yield trials conducted in Nigeria. These spontaneous polypoloids provide greater genetic variation and offer an opportunity to breed radically new cassava varieties. Approaches for isolating and utilizing the polyploid cassava clones for varietal and population improvement are discussed.