Breeding value for cassava mosaic disease resistance analyzed in a seedling nursery Kulakow Peter A. 1, Bakare Moshood A. 1, Agbona Afolabi 1, Parkes Elizabeth Y. 1, Ceballos Hernan 2, Rabbi Ismail Y. 1, Olaniyo Esther 1, Andrew Ikpan S. 1, Iluebbey Peter O. 1, Lava Kumar P. 1 and Nokoe K. Sagary 3 1 Cassava Breeding program IITA Ibadan, Nigeria 2 CIAT, Cali Colombia 3 Catholic University of Eastern, Africa, Nairobi Kenya World Congress on Root and Tuber Crops Nanning, Guangxi, China, January 18-22, 2016
Problem statement Ø Cassava Mosaic Disease (CMD) is serious threat to cassava production in Africa and has been a major objective in breeding for improved varieties. Ø CMD is by caused by several begomoviruses and is transmitted by the white fly (Bemisia tabasci) Ø Most exotic germplasm introduced from Latin America to Africa is highly susceptible to CMD Ø Breeding Resistant varieties has provided effective control of CMD
Cassava mosaic disease ACMV only ACMV+EACMV ACMV+EACMV
Host resistance in controlling CMD Resistant Susceptible CMD 1 quantitative resistance (recovery resistance) Not very effective against mixed infections and some severe strains CMD 2 High levels of resistance (qualitative!) Offers resistant to single and mixed infections of all species
Problem statement Ø However, recent genomic evidence has show the genetic base of CMD resistance is narrow with most resistance mapping to Chromosome12 of the newest version of the cassava genome. Ø Our challenge is to find new sources of CMD resistance to broaden the sources of resistance in Africa and to pre-emptively breed for CMD resistance in Asia and Latin America
Materials and Methods Ø Since CMD is not transmitted through botanic seed. Seedling nurseries provide an opportunity to evaluate parents and progeny for resistance to CMD beginning with disease free seedlings. Ø In 2009 IITA received 5000 botanic seed from CIAT with a high beta-carotene background Ø In January 2010, at one month after transplanting seedlings to the field, 2472 plants had an average cmd severity of 3.43 and cmd incidence of 78% Ø 42 plants eventually flowered and were used in in crosses as male parents to sources of CMD resistance.
Ø A few plants of these parents and other selected CIAT seedlings have been clonally propagated as genetic stocks with good cmd resistance. These have been used in further crosses. Ø An unreplicated seedling nursery trial established with 158 female parents crossed 56 male parents. Ø There are 418 full-sib crosses established with and average progeny size of 32 plants per family resulting in a seedling nursery with 13,250 plants. Seedlings were transplanted in April 2015 Ø CMD susceptible clone (TMEB117) was used as a spreader
Ø All individual seedlings were tagged to facilitate data collection. Ø CMD severity was scored monthly from 2 to 6 months after planting. Ø Binary response of CMD incidence was recorded based on the presence or absence of leaf symptoms Ø The probability of CMD infection was fitted to mixed effects logistic regression model in SAS with the GLIMMIX procedure
Ø Fixed factors in the model q Block design factor q Northing and easting as covariates Spatial effect Ø Random factors in the model q Family q Female parent q Male parent
Results Distribution of families with or without CIAT parents/grandparents Group No. family Family % Mean cmdi std No_CIAT_parent/grandparent 96 22.9 0.30 0.06 One_grandparent_from_CIAT 143 34.0 0.30 0.06 One_parent_from_CIAT 153 36.4 0.29 0.04 Two_grandparents_from_CIAT 18 4.3 0.30 0.07 Two_parents_from_CIAT 10 2.4 0.32 0.04
Estimates of variance component parameters Month of CMD evalua/on Variance component 2 3 4 5 6 Family 0.35±0.07 0.20±0.05 0.35±0.06 0.22±0.06 0.24±0.06 Female 0.24±0.08 0.23±0.07 0.18±0.07 0.25±0.08 0.15±0.06 Male 0.33±0.16 0.27±0.12 0.36±0.14 0.58±0.21 0.45±0.17
Estimates of Spatial fixed effects distance to CMD spreader Effect Month Estimate Std Error t Value Pr > t 95% LCL 95% LCL Northing 0.04 0.01 3.01 0.00 0.01 0.07 2 Easting -0.01 0.01-1.06 0.29-0.02 0.00 Northing 0.03 0.01 2.63 0.01 0.01 0.06 3 Easting 0.01 0.00 1.38 0.17 0.00 0.02 Northing 0.03 0.01 2.35 0.02 0.00 0.05 4 Easting 0.00 0.00-0.54 0.59-0.01 0.01 Northing 0.02 0.01 1.95 0.05 0.00 0.05 5 Easting 0.00 0.00 1.04 0.30 0.00 0.01 Northing 0.03 0.01 2.14 0.03 0.00 0.05 6 Easting 0.00 0.00-0.52 0.60-0.01 0.01
Trends of CMD infection by CIAT parent groups over months
Obs male N BLUP Estimate StdErrPred predicted_prob actual cmd6i 1 IBA141088 327 1.14 0.27 0.44 0.70 2 IBA141104 268 1.07 0.29 0.43 0.78 3 IBA141093 15 1.05 0.58 0.42 0.93 4 IBA141103 26 0.99 0.49 0.41 0.85 5 IBA141095 150 0.92 0.32 0.39 0.73 6 IBA121636 51 0.83 0.36 0.37 0.65 7 IBA141098 15 0.77 0.53 0.36 0.80 8 IBA141107 6 0.75 0.62 0.35 0.83 9 SM3444-2 94 0.73 0.49 0.35 0.34 10 IBA070593 27 0.52 0.46 0.30 0.33 48 UBJ120003 3233-0.60 0.23 0.12 0.22 49 GM3594-12 349-0.61 0.31 0.12 0.14 50 IBA011371 51-0.62 0.45 0.12 0.12 51 IBA121639 42-0.68 0.48 0.11 0.21 52 SM3661-19 902-0.84 0.35 0.10 0.14 53 GM3667-40 36-0.87 0.50 0.10 0.31 54 GM3667-88 30-0.88 0.54 0.10 0.13 55 IBA070539 29-1.05 0.54 0.08 0.07 56 SM3666-12 1311-1.16 0.30 0.07 0.16 57 SM3666-19 81-1.18 0.45 0.07 0.11
Conclusions Ø Ø Ø The trends of the CMD infection is relatively similar across the families with/without CIAT parent/grandparent Families with CIAT and non-ciat parents exhibited low likelihood of CMD infection At least 6 genotypes derived from botanic seed received from CIAT appear to have good breeding value for CMD resistance. Genotype Pedigree GM3594-12 GM 1548-33 X GM 1561-11 SM3661-19 GM3667-40 GM 1551-36 X GM 1561-11 GM3667-88 GM 1551-36 X GM 1561-11 SM3666-12 SM3666-19
Conclusions 1. The spatial fixed effects of northing and easting distance from plot to CMD spreader had no significant influence on predicted probability of CMD infection suggesting that inoculum spread had sufficient for even spread of disease 2. The fittings of GLMMs to disease status (0/1) gave BLUPs estimate for families and parents from which predicted probability of CMD infection can be estimated 3. The family and parents accounted for significant amount of variation in predicted probability of CMD infection
Conclusions 4. Seedling nurseries likely can provide useful information on the breeding value of parents. 5. It appears that CMD resistance can be recovered from Latin American germplasm. Further exploration of the genetic background of these genotypes is needed. 6. Further exploration of Latin American germplasm as a source for CMD resistance is warranted.
Acknowledgments We appreciate the support of Harvest Plus and its partners for support of biofortification breeding in cassava The CGIAR research program on Roots, Tubers and Bananas has provided the foundational support for cassava breeding that makes this work possible. Alfred Dixon and Paul Ilona developed the breeding materials through 2009 and initiated the collaboration with CIAT on biofortified cassava.
Thank you