Breeding for Drought Tolerance in Cowpea [vigna Unguiculata (L.) Walp.] Using Marker Assisted Backcrossing
ABSTRACT
The potential of cowpea to address food security in Burkina Faso in particular is well established. However, there is limited information on drought tolerance and diversity in the germplasm in Burkina Faso and farmers’ perceptions on the effects of drought and their varietal preferences are not known. The present study was, therefore, conducted to: (1) identify farmers’ perceptions on the impact of drought on cowpea production and identify their preferences regarding cultivars and traits, (2) identify drought tolerant varieties in cowpea germplasm, (3) determine single nucleotide polymorphisms (SNPs) based genetic diversity in the cowpea germplasm, and (4) implement marker-assisted backcrossing to transfer yield and stay-green QTLs into Moussa local, a farmer preferred landrace. A participatory rural appraisal (PRA) was conducted to identify farmers’ perceptions on the impact of drought on cowpea production. This study established that farmers have a deep knowledge about cowpea production constraints. Limited access to seed of improved variety was ranked as the most important constraint in all the areas where the study was conducted. Drought was classified among the four most important constraints to cowpea production in the three districts where the PRA was conducted. The preferred grain traits for all regions were white colour, large seeds with a rough texture for food and market purposes, except for the northern region where brown grain colour was preferred for food. The identification of drought-tolerant varieties in cowpea germplasm through field screening of fifty genotypes and the use of selection indices revealed wide genotypic variability among the tested germplasm. Biplot displays indicated that the genotypes could be grouped into four categories according to their drought tolerance and yielding ability as indicated below: high yielding-drought tolerant (group A), high yielding-drought susceptible (group B), low yielding-drought tolerant (group C), and low yielding-drought susceptible (group D). Genotypes like Djouroum local, KVx404-8-1, IT98K-1111-1, Gorom local, CB27, IT93K-693-2, Mouride, and KVx61-1 were clustered in group A, that is they were high yielding and drought tolerant. The stress tolerance index was the best criterion
for assessing genotypes for variability to drought tolerance because it enabled the identification of high yielding and drought tolerant genotypes. Genetic diversity was assessed using 181 SNP markers on 50 cowpea lines. The phylogenetic pattern of this germplam revealed seven clusters. The lines were almost grouped based on their geographical origin, and the breeding background. Thus, materials which originated from Burkina Faso were clustered in the same group while those from IITA/Nigeria were also almost all clustered in the same group. The genetic distance was low (≤0.29) suggesting a narrow genetic base in the cowpea germplasm used in this study. SNPs were efficient in the study of the diversity and a core collection of 20 lines was generated for further use in the breeding program. Marker-assisted backcrossing (MABC) was used to transfer QTLs for yield under drought and stay- green into Moussa local, a farmer preferred landrace. Two backcrosses assisted by SNP markers in foreground and background selections were sufficient to select for QTLs presence and to recover the background of Moussa local, the recurrent parent. The BC3F1s were selfed and six BC3F2s were evaluated for preliminary yield under drought stress and non-stress conditions. Out of the six, three MABC selected lines were promising and yielded better than the check and the parents. From these recombinant lines, several high yielding lines are likely to be developed for release in the near future. Most of them could be used in intercropping which will make great impact on cowpea production in Burkina Faso. In general, potential parents for genetic improvement for yield and drought tolerance were identified. However, further studies for assessing yield stability of cowpea genotypes are necessary and could be achieved by including more seasons and sites to get a better understanding of the genotype × environment interaction and yield stability of cowpea in Burkina Faso for all the materials identified including the MABC lines.
Key words: Burkina Faso, farmers, drought tolerance, cowpea, genotypes, genetic distance, SNPs, marker-assisted backcrossing, Participatory Rural Appraisal.
CHAPTER ONE
1.0. GENERAL INTRODUCTION
Cowpea (Vigna unguiculata (L.) Walp) is one of the most important grain legumes grown in the semi-arid regions of Africa. Out of the world’s total production area of 14 million hectares, West Africa accounts for about 9 million ha (Singh et al., 2003). Cowpea is mostly grown in the semi- arid region of West Africa (Ehlers and Hall, 1997) because of its large adaptation to climatic conditions. It is grown in over 9.5 million ha with a production of 2.9 million tons (Omo-Ikerodah et al., 2005). In the USA, under optimum conditions, the average yield of cowpea is 7000 kgha-1 whereas in Africa, average yield of the resource poor farmer is 300 kgha-1 (Ehlers and Hall, 1997; Tignegre, 2010).
Burkina Faso is ranked amongst the top three cowpea producers in West Africa with a production of 580,000 tons in 2013 after Nigeria (2.50 million tons) and Niger (1.30 million tons) (Faostat, 2014). Cowpea production has increased from 276,349 tons in 2004 to 580,000 tons in 2013 with rapid decline in some years as a result of drought occurrence. Similarly, area under cultivation increased from 588,000 ha (2004) to 1,200,500 ha (2013) indicating that increase in production was associated with increase in area under cultivation. However, cowpea has contributed about 20 billion CFA (32,542,604 USD) to Burkina Faso’s net domestic product for the last ten years (Statistika, 2002). It has recently been recognized by the government of Burkina Faso as a strategic crop that would contribute to achieving food security and alleviating poverty, due to its market potential.
Cowpea production is suitable for subsistence farming systems in which low inputs are involved due to its ability to thrive on relatively poor soil (Pasquet, 1999; Pronaf, 2003). It has high level of adaptation due to its inherent ability to withstand drought, tolerate shade, and fix atmospheric nitrogen (Singh, 1997).isIt the first crop harvested during the cropping season before staple cereals crops (largely pearl millet and sorghum) and, therefore, referred to as a ‘‘hungry-season crop’’(Agbicodo et al., 2009). It is an important cash-crop and source of nutrients (protein 23- 25%) to the rural communities in tropical Africa (Ehlers and Hall, 1997; Ouedraogo, 2001). After harvesting the pods, the fodder is also harvested and used as feed for livestock. In terms of utilization, the diversity of diets based on cowpea, and the short cooking time renders cowpea popular for rural people and low income workers in towns (Tignegre, 2010). Leaves, fresh peas and fresh pods are also consumed (Ehlers and Hall, 1997). However, production is affected by several biotic and abiotic factors that lead to severe yield reduction at the smallholder farmer level (Ehlers and Hall, 1997).
Drought is one of the most important constraints threatening the food security of the world (Barters and Nelson, 1994). Cowpea production in Burkina Faso is hampered by recurrent drought. The rainfall patternsbheaevneirregular and below normal throughout the semi-arid zones of West Africa including Burkina Faso. In the Sudan and Sahelian semi-arid regions, the frequency and intensity of drought have increased over the last 30 years (Hall et al., 2003) due to climatic changes and human activities (Wittig et al., 2007). Estimates on yield reduction due to terminal drought range from 21-30% between stressed and non-stressed conditions (Chiulele, 2010). However, yield losses in plant production depend on geographical region and length of cropping season (Sabaghpour et al., 2006). Drought spells in farmers’ field has results in reduction of yields of
available genotypes. Most of these genotypes are susceptible to drought. Drought can strike at anytime, anywhere. Plants are most prone to damage due to limited water during flowering and pod setting stages (Bahar and Yildirim, 2010). Recently drought episodes (1984, 1991, 2004, and 2011) resulted in important crop yield losses and famine in Burkina Faso. The most recent drought was in 2011. In that year, a deficit of about 154462 tons was recorded in crop production
(http://fr.allafrica.com/stories/) in Burkina Faso. Therefore,iist desirable to improve these adapted
genotypes for tolerance to drought in order to obtain high and stable yields.
Until recently, the strategy for improving cowpea varieties in Burkina Faso for drought depended on the use of drought avoidance mechanism through the use of early maturing varieties. These varieties are meant to attain physiological maturity before drought occurs. However, the erratic rainfalls at the beginning and towards the end of the rainy season affect the early maturing varieties resulting in a substantial reduction in grain yield and total biomass production (Agbicodo et al., 2009). Therefore, the use genetic tolerance would be the best alternative for reducing the effects of drought in cowpea. Despite the genetic variability existing within wild Vigna species, improved varieties, and landraces in Burkina Faso (Tignegre, unpublished data), no in-depth investigation has been done to determine their tolerance to drought. Studies on genetic variability and diversity in drought tolerance need to be conducted to assist in the identification of suitable parents to improved cowpea for drought tolerance.
Drought tolerance in cowpea is governed by multiple genes whose effects are often masked by or interact with the environment (Timko and Singh, 2008). As such, breeding for drought using conventional methodologies is not easy to achieve. Molecular markers can be used to identify
regions of the genome that harbor the genes that contribute to drought tolerance (Timko and Singh, 2008). If the most important genes can be tagged with molecular markers; they could be reliably introgressed into highly desirable cultivars that are susceptible to drought therefore, improving their tolerance to drought. The availability of high throughput genotyping platforms provides new opportunities for improvement of complex traits like drought tolerance through marker-assisted breeding (MAB).
Cowpea remained among “orphan crops” with limited genomic resources for long but significant genomic resources have recently been developed and made available to the public. These new development include high quality consensus genetic map (Muchero et al., 2009a; Lucas et al., 2011), high-throughput genotyping systems based on the Illumina GoldenGate and KBiosciences KASPAR systems, fingerprints of more than 600 potential parent lines, and a physical map (Http://Phymap.Ucdavis.Edu/Cowpea/, 2013). With the map density now available in cowpea (average marker density of 0.6 cM and no gap > 4 cM), in many cases it will be possible to identify flanking markers. By using markers that flank the target drought tolerance QTLs, linkage drag can be minimized. These advances in plant molecular genetics have provided plant breeders with powerful tools to identify and select Mendelian components underlying both simple and complex agronomic traits (Ribaut and Hoisington, 1998). SNP markers tightly linked to drought tolerance QTLs have been identified in cowpea (Muchero et al., 2010). These markers will be useful in the introgression of drought tolerant genes into desirable cowpea genotypes using MAB.
The overall research goal of the study was to identify promising cowpea genotypes that are drought tolerant and high yielding that would contribute to food security.
The specific objectives were to:
- Determine farmer perceptions on the impact of drought in cowpea
- Identify sources of tolerance to drought stress in the cowpea germplasm
- Determine the SNP-based genetic diversity of a set of cowpea germplasm
- Introgress drought tolerant (stay green and yield) QTLs into Moussa local, a farmer preferred cowpea genotypes using marker-assisted
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