A Review of Molecular Makers Applied in Cowpea (Vigna unguiculata L. Walp.) Breeding

Journal of Life Sciences 6 (2012) 1190-1199 A Review of Molecular Makers Applied in Cowpea (Vigna unguiculata L. Walp.) Breeding Huaqiang Tan, Manman...
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Journal of Life Sciences 6 (2012) 1190-1199

A Review of Molecular Makers Applied in Cowpea (Vigna unguiculata L. Walp.) Breeding Huaqiang Tan, Manman Tie, Qian Luo, Yongpeng Zhu, Jia Lai and Huanxiu Li College of Horticulture, Sichuan Agricultural University, Ya’an 62504, Sichuan, China

Received: June 12, 2012 / Accepted: August 13, 2012 / Published: November 30, 2012. Abstract: In recent years, with the rapid development of molecular biology, molecular markers have been widely used in genetic breeding of various crops including cowpea. However, molecular researches in cowpea are lack of systematic summary. This review presents an overview of accomplishments on different aspects of molecular markers in cowpea genetic breeding, such as genetic diversity analysis, genetic linkage map construction, QTL mapping, etc. Furthermore, it provides the discussion of some existing problems about molecular markers applied in cowpea breeding and the prospect of the future development. The authors find that SSR is the most frequently used molecular marker, while SNP has not been used in the genetic diversity analysis of cowpea. And the authors also conclude that more QTL of cowpea should be located and more molecular markers linked to resistance gene should be found. This will be useful for scientists and breeders to research cowpea with the aid of molecular markers, thus accelerating improvement of cowpea varieties. Key words: Molecular markers, cowpea, breeding, genetic diversity, review.

1. Introduction Cowpea (Vigna unguiculata L. Walp.), which originates in Africa, is an important grain legume growing in tropical and subtropical regions, including Asia, Africa, Central and South America, the United States and part of the southern Europe. The planting area is more than 12.5 million hectares worldwide, with an annual production of more than 3 million tons [1]. The drier savanna and the Sahelian region of West and Central Africa produce about 70% of worldwide cowpea production, with Nigeria, Niger and Brazil being the largest producers [2]. Cowpea is called “poor man’s meat” [3] because the seed protein contents range from 23% to 32% of seed weight rich in lysine and tryptophan, and a substantial amount of mineral and vitamins (folic First author: Huaqiang Tan, master, research field: application of biological technology in horticulture plant. E-mail: [email protected]. Corresponding author: Huanxiu Li, professor, research field: application of biological technology in horticulture plant. E-mail: [email protected].

acid and vitamin B) necessary for preventing birth defect during the pregnancy stage [4]. In many parts of West Africa, cowpea hay is also critical in the feeding of animals during the dry season [5]. In addition, cowpea is a nitrogen-fixing plant, when used in rotation with cereal crops it can help restore soil fertility [6]. Therefore, cowpea can play an important role in the development of agriculture. The development of cowpea industry relies heavily on the improvement of existing cultivars and breeding of new varieties. Traditional selection mainly depends on the phenotypic variation. However, morphological markers are easily influenced by the environment, and some of them have epistatic effects [7]. Simultaneously, conventional breeding program requires selection on many generations of the material, leading to the reduction of reliability and efficiency. DNA molecular markers are genetic markers based on individual nucleotide sequence variation, which are the direct reflection of genetic polymorphisms at the DNA level. Compared with morphological markers,

A Review of Molecular Makers Applied in Cowpea (Vigna unguiculata L. Walp.) Breeding

cytological markers and biochemical markers, DNA molecular markers have some unique advantages, its multi-locus nature as well as high reproducibility, simplicity and low cost make it particularly attractive for analyzing a large number of samples with narrow genetic variation [8]. The technology mainly consists of RFLP (restriction fragment length polymorphism), AFLP (amplified fragment length polymorphism), SSR (single sequence repeat), RAPD (random amplified polymorphic DNA), SNP (single nucleotide polymorphisms), and so on. They are widely used in genetic diversity research, variety identification, phylogenetic analysis, gene mapping and resource classification, etc. [9]. The objective of this paper is to summarize the main previous achievements on molecular makers used in cowpea breeding and discuss the existing problem and the prospect in its application, in order to provide a reference for scientists who are engaged in this field.

2. Application of Molecular Markers in Cowpea Since the gene theory was put forward,genotypic selection has replaced phenotypic selection gradually. Since then, DNA molecular markers are becoming a research hotspot. The research on AFLP, SSR and RAPD is changing rapidly. 2.1 Analysis of Genetic Diversity For

cowpea

breeding,

the

genetic

diversity

information is extremely important, which is the basis of breeding and genetic research. Accurate assessment of genetic variability is important for the preservation and

utilization

of

germplasm

resources,

and

improvement of cultivars. For this reason, scholars all over the world have made extensive and in-depth research on the genetic diversity of cowpea. 2.1.1 The Application of RAPD RAPD is widely used in cowpea genetic analysis because it is simple and little DNA is required. The

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RAPD technology was proved to be a useful tool in the characterization of the genetic diversity among cowpea cultivars by Zannou et al. [10]. In their study, RAPD markers were used to evaluate the genetic diversity in 70 cowpea accessions collected throughout Benin. The genetic diversity was very large. Based on the molecular variance, the fixation index suggested a large differentiation of cowpea cultivars in Benin. Malviya et al. [11] used 18 sets of RAPD markers to analyse the genetic diversity among ten Indian cultivars of cowpea. The variation in genetic diversity among these cultivars ranged from 0.1742 to 0.4054. Cluster analysis using UPGMA revealed two distinct clusters I and II comprised of two and seven cultivars, respectively. Cultivar IC-9883 was found to be unique. Ba et al. [12] analysed 26 domesticated and 30 wild cowpea species from west, eastern and southern Africa. Wild species in eastern Africa had more polymorphisms, which may be the origin of V. unguiculata var. spontanea. Nkongolo et al. [13] determined the pattern and extend of RAPD marker variation within and among cowpea populations from different agroecological zones, a general lack of agreement between clustering and morphological features was observed. Chen et al. [14] analysed 40 yardlong beans collected from Jianghan University by RAPD makers. A total of 30 primers generated 140 polymorphic RAPD bands. The various numbers of bands amplified by RAPD among the varieties were noticed. 2.1.2 The Application of SSR SSR is the most frequently used marker in the genetic diversity analysis of cowpea. The earliest cowpea SSR research is conducted by Li et al. [15], and 27 SSR primers have been developed. After that, SSR research on cowpea from different areas, mainly Africa and Asia, has been carried out. Africa is the diversity center of wild cowpea, which was proved by Ogunkanmi et al. [16] with SSR analysis. Asare et al. [17] utilized SSR molecular markers to evaluate

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A Review of Molecular Makers Applied in Cowpea (Vigna unguiculata L. Walp.) Breeding

genetic diversity and phylogenetic relationships among 141 cowpea accessions collected throughout the nine geographical regions of Ghana. PIC (the polymorphism information content) varied from 0.07 to 0.66 with an average of 0.38. The Ghanaian cowpea accessions clustered into five main branches, each of which was loosely associated with the geographical regions from which samples were obtained. Badiane et al. [18] assessed the genetic diversity and phylogenetic relationships among 22 local cowpea varieties and inbred lines collected throughout Senegal by SSR markers, and developed a set of 44 polymorphic primer combinations from cowpea genomic or expressed sequence tags, the PIC value ranging from 0.08 to 0.33. The local varieties clustered in the same group, except 53-3, 58-53, and 58-57; while Ndoute yellow pods, Ndoute violet pods and Baye Ngagne were in the second group. Sawadogo et al. [19] evaluated the genetic diversity and phylogenetic relationships among cowpea genotypes used in breeding for resistance to Striga gesnerioides in Burkina Faso using simple SSR molecular markers. Very few primer combinations showed polymorphic bands capable of discriminating Striga-resistant from susceptible cultivars, which revealed a high efficiency of SSR markers. Although Asia is one of the major cowpea growing areas, genetic diversity researches on cowpea in Asia are still very little. Lee et al. [20] estimated the genetic diversity of 492 Korean cowpea landrace accessions using six SSR markers. The mean of Weir’s gene diversity was 0.665 from all the accessions. Cowpea gene diversity of six local provinces in Korea ranged from 0.370 in accessions of Gangwon to 0.680 in Jeonra provinces. Especially SSR markers VM36 and VM39, which seem to be good markers to distinguish the Gangwon accessions from others by occurring at a specific locus with higher than 78% of allele frequency, have been found. Xu et al. [21] assessed the genetic diversity of asparagus bean cultivars from different geographical origins in China by

EST-derived and GSS-derived SSR markers. PCA (principal coordinate analysis) and phylogenetic clustering based on 62 alleles detected by 14 polymorphic SSR markers distinguished ssp. unguiculata and sesquipedialis into separate groups. Improved cultivars of asparagus bean in China generally had a narrow genetic basis compared with landraces. This suggested that breeding programs of asparagus bean need to utilize landrace germplasm to enhance genetic variability, ensure long-term gains from selection, and reduce genetic vulnerability to pathogen or pest epidemics. Xu et al. [22] extracted the DNA of a total of 316 cultivated cowpea resources from China, Africa and other Asian countries, which were amplified by SSR to study their genetic diversity. The result showed that the genetic diversity of foreign accessions is higher than that of the domestic accessions. Cowpea in Guangxi and Hubei province has a rich genetic diversity, but a relatively low genetic diversity was found in Anhui, Jilin, Heilongjiang and Shanxi province. 2.1.3 The Application of AFLP AFLP is recognized as one of the most efficient molecular markers. Coulibaly et al. [23] employed AFLP to evaluate genetic relationships within a total of 117 cowpea accessions to assess the organization of their genetic diversity. Wild annual cowpea (var. spontanea) was more diverse than domesticated cowpea. Wild cowpea in eastern Africa was more diverse than in western Africa, suggesting an eastern African origin for the wild taxon. Fang et al. [24] examined genetic relationships among 60 advanced breeding lines from six breeding programs in West Africa and USA, and 27 landrace accessions from Africa, Asia, and South America. AFLP markers with six near infrared fluorescence labeled EcoRI + 3/1bases/MseI + 3/1bases primer sets were used in the study. Principal coordinates analysis showed clustering of breeding lines by program origin, indicating lack of genetic diversity compared to potential diversity.

A Review of Molecular Makers Applied in Cowpea (Vigna unguiculata L. Walp.) Breeding

2.1.4 The Application of Combinative Markers The advantages of combinative markers are that they could be analyzed both separately and in combination, which makes the result more reasonable. Diouf et al. [3] used RAPD and SSR techniques to study the genetic diversity in local cowpea varieties and breeding lines from Senegal. Microsatellite markers are found to be more effective than RAPD in determining the relationship among cowpea accessions and varieties. Tosti et al. [25] studied three neighbouring cowpea landraces currently cultivated in central Italy by AFLP and SAMPL markers to determine the distribution of genetic variation within and among them. The three landraces studied, although relatively similar, were highly different from one another as shown by the data obtained from the AFLP and SAMPL markers. Gillaspie et al. [26] utilized AFLP and SSR markers to assess genetic diversity and relatedness between Vigna unguiculata subspecies. Three AFLP primer combinations and 10 SSR primer sets successfully identified closely related accessions, and the presence of heterogeneity in some accessions. Results of cluster analysis between molecular markers and morphological traits are usually lack of consistency [13]. Reasons for this could be: the limited number of traits observed, the limited variation for the traits, the number of underlying genes for the traits, which may also be limited, and possible epistatic interactions among the genes [27]. In cowpea genetic breeding and evaluation of germplasm resources, a combination of molecular markers and classical markers is essential. Tantasawat et al. [8] estimated genetic diversity and relatedness of 23 yardlong bean (Vigna unguiculata spp. sesquipedalis) accessions and 7 accessions of a hybrid between cowpea (V. unguiculata spp. unguiculata) and dwarf yardlong bean in Thailand by morphological characters, SSR and ISSR markers. Five morphological characters were diverse among most accessions. However, five groups of 2-3 accessions

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could not be distinguished from one another based on these morphological characters alone. The comparison of average marker index of the multilocus marker and mantel test indicated higher efficiency of ISSR for estimating the levels of genetic diversity and relationships among yardlong beans and dwarf yardlong beans in the study. Ghalmi et al. [28] compared 20 landraces of cowpea scattered throughout Algeria through morphological and genetic characterization. Despite the absence of significant correlation between morphological and RAPD data, significant correlations between morphological data and both ISSR and a combined RAPD-ISSR dataset were noted. A conclusion had been made that ISSR markers were better linked to morphological variation than RAPD markers. 2.2 Construction of Genetic Linkage Map Genetic map refers to chromosomal linear linkage map which uses chromosome recombinant exchange rate as relative length units and mainly consists of genetic markers. It can be used to locate and mark the target gene to promote the application of marker-assisted breeding in practice. At the same time, it reveals the genetic basis of traits controlled by multiple genes and provides an important tool for map-based cloning. Therefore, building a high-density genetic linkage map is of great significance. The cowpea genetic linkage map is mainly constructed by a cross between a wild species or a cultivated species in the wild type and a cultivar because of its relatively narrow genetic background. There are not many current cowpea genetic maps which are usually constructed with RIL (recombinant inbred lines), the most commonly used mapping population (Table 1). The first map to be constructed was based mainly on the segregation of RFLP markers in the progeny of a cross between an improved cultivar and a putative wild progenitor type (Vigna unguiculata subsp. dekindtiana) [29]. The map consisted of 92 markers placed in eight linkage groups

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A Review of Molecular Makers Applied in Cowpea (Vigna unguiculata L. Walp.) Breeding

that spanned a total genetic distance of 684 cm. After that, Menendez et al. [30] constructed a genetic linkage map within the cultivated gene pool of cowpea. The map consisted of 181 loci, comprising 133 RAPDs, 19 RFLPs, 25 AFLPs, three morphological markers, and a biochemical marker (dehydrin). These markers identified 12 linkage groups spanning 972 cm with an average distance of 6.4 cm between markers. On the basis of the two maps above, Ouedraogo et al. [31] constructed an improved genetic linkage map, which was based on the segregation of various molecular markers and biological resistance traits. The new genetic map of cowpea consists of 11 LGs (linkage groups) spanning a total of 2670 cm, with an average distance of 6.43 cm between markers. And they also discovered a large, contiguous portion of LG1 that had been undetected in previous mapping work. This region, spanning about 580 cm, was composed entirely of AFLP markers. Subsequently, cowpea genetic linkage maps have been constructed one after another. A genetic linkage map of yardlong bean based on SSR makers from related Vigna species had been developed by Kongjaimun et al. [32]. The markers were clustered into 11 linkage groups spanning 852.4 cm in total length with a mean distance between adjacent markers of 3.96 cm. Andargie et al. [33] constructed a genetic linkage map using SSR markers and a RI (recombinant inbred) population of 159 individuals derived from a cross between the breeding line 524B and 219-01. 202 polymorphic SSRs were used to construct a genetic map consisting of 11 linkage

groups spanning 677 cm, with an average distance between markers of 3 cm. Xu et al. [34] reported the first genetic map of asparagus bean based on SNP and SSR markers. The current map consists of 375 loci mapped onto 11 linkage groups, with 191 loci detected by SNP markers and 184 loci by SSR markers. The overall map length is 745 cm, with an average marker distance of 1.98 cm. Muchero et al. [35] developed 1536 EST-derived SNPs and applied to 741 recombinant inbred lines from six mapping populations to construct a cowpea genetic map. Of these SNPs, 928 were incorporated into a consensus genetic map spanning 680 cm with 11 linkage groups and an average marker distance of 0.73 cm. The construction of current cowpea genetic map is mainly based on efficient molecular markers such as AFLP, SSR and SNP. RAPD markers are generally not used to construct genetic maps due to the poor reproducibility. High-density genetic map provides a powerful tool for analysing the heredity of target gene, monitoring specific genes or genomic regions transmitted from parent to next generation, as well as map-based cloning. Therefore, more high-density genetic map of cowpea should be developed by taking advantages of molecular markers. 2.3 Molecular Markers Linked to Resistance In breeding program, using molecular markers to select the target trait is called MAS (marker-assisted selection), which is the main application of molecular markers. In Africa the parasitic weed Striga gesnerioides is the main biotic factor restricting yield

Table 1 Some genetic linkage map of cowpea. MP: mapping population; AD: average distance; LG: number of linkage group; RIL: recombinant inbred lines; F2: F2 population. AD (cm)

LG

References

680

7.70

11

Young et al. [29]

IT84S-2049; 524B

2670

6.43

11

Ouedraogo et al. [31]

Six pairs of parents

680

0.73

11

Muchero et al. [35]

Markers used

MP

Parents

RFLP

F2

IT84S-2246-4; NI 963

AFLP

RIL

SNP

RIL

Length (cm)

SSR

RIL

219-01; 524B

677

3.00

11

Andargie et al. [33]

SSR

RIL

JP81610; TVnu457

852.4

3.96

11

Kongjaimun et al. [32]

SNP, SSR

RIL

Zhijiang282; ZN016

745

1.98

11

Xu et al. [34]

RAPD, RFLP, AFLP

RIL

IT84S-2049; 524B

972

6.40

12

Menendez et al. [30]

A Review of Molecular Makers Applied in Cowpea (Vigna unguiculata L. Walp.) Breeding

of cowpea. Growing cultivars that have resistance to the parasitic weeds is the best way. Searching for more molecular markers tightly linked to the resistance traits against parasitic of cowpea will greatly improve breeding efficiency. Ouedraogo et al. [36] identified three AFLP markers and seven AFLP markers that were linked to Rsg2-1, a single dominant gene controlling resistance to S. gesnerioides race 1, and Rsg4-3, a single dominant gene controlling resistance to S. gesnerioides race 3, respectively. Both of them were located within linkage group 1 of the cowpea genetic map. Boukar et al. [37] identified four AFLP markers, and mapped 3.2, 4.8, 13.5 and 23.0 cm, respectively, from Rsg1, a gene in IT93K-693-2 that gives resistance to race 3 of S. gesnerioides. The AFLP fragment from marker combination E-ACT/M-CAC, which was linked in coupling with Rsg1, was cloned, sequenced, and converted into a SCAR (sequence characterized amplified region) marker named SEACTMCAC83/85, which was co-dominant and useful in breeding programs. Rust disease, incited by the fungus Uromyces vignae, is one of the major diseases in cowpea production. Li et al. [38] determined that rust resistance was controlled by a single dominant gene designated Rr1. An AFLP marker (E-AAG/M-CTG) was converted to a SCAR marker, named ABRSAAG/CTG98, and the genetic distance between the marker and the Rr1 gene was estimated to be 5.4 cm. Aphid not only hinders growth, transmits virus, but also causes abnormal of flower, leaf and bud. Yield losses of up to 35% and 40% have been attributed to aphid infestation in Africa and Asia respectively [39]. Myers et al. [40] found one RFLP marker, bg4D9b, to be tightly linked to the aphid resistance gene (Rac1). The close association of Rac1 and RFLP bg4D9b presented a real potential for cloning this insect resistance gene. 2.4 QTL Mapping The location of genes controlling quantitative traits

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in the genome is known as QTL (quantitative trait loci). QTL could be detected by employing molecular markers in genetic linkage analysis, i.e. QTL mapping. With the help of molecular markers linked to QTL, the heredity of some related QTL could be tracked and the ability of genetic manipulation to QTL is greatly enhanced, thus improving the accuracy and predictability to select genotypes with superior quantitative trait. Therefore, the QTL mapping of cowpea is an important basic work (Fig. 1). At present, many scholars have utilized different genetic maps based on molecular markers to locate many QTL associated with cowpea yield. Kongjaimun et al. [32] developed a genetic linkage map of yardlong bean using 226 SSR makers from related Vigna species and to identify QTLs for pod length. One major and six minor QTLs were identified for pod length variation between yardlong bean and wild cowpea. Andargie et al. [33] identified the QTLs of cowpea agronomic traits related to domestication (seed weight, pod shattering) by SSR markers. Six QTL for seed size were revealed with the phenotypic variation ranging from 8.9%-19.1%. Four QTL for pod shattering were identified with the phenotypic variation ranging from 6.4%-17.2%. The QTL for seed size and pod shattering mainly clustered in two areas of LGs 1 and 10. Fatokun et al. [41] developed genomic maps for cowpea based on RFLP markers. Using these maps, major QTLs for seed weight had been identified. Muchero et al. [42] reported the mapping of 12 QTL associated with seedling drought tolerance and maturity in a cowpea recombinant inbred (RIL) population. Regions harboring drought-related QTL were observed on linkage groups 1, 2, 3, 5, 6, 7, 9, and 10 accounting for between 4.7% and 24.2% of the phenotypic variance. Further, two QTL for maturity were mapped on linkage groups 7 and 8 separately from drought-related QTL. Some QTL of resistance to disease and insects have also been identified. CoBB (cowpea bacterial blight), caused by Xanthomonas axonopodis pv. vignicola

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Fig. 1

A Review of Molecular Makers Applied in Cowpea (Vigna unguiculata L. Walp.) Breeding

QTL mapping of cowpea. LG: linkage group.

(Xav), is a worldwide major disease of cowpea. Agbicodo et al. [43] used a SNP (single nucleotide polymorphism) genetic map with 282 SNP markers constructed from the RIL population to perform QTL analysis. Three QTLs, CoBB-1, CoBB-2 and CoBB-3 were identified on linkage group LG3, LG5 and LG9, respectively. Besides, Muchero et al. [44] identified the QTL for Macrophomina phaseolina resistance and maturity in cowpea with SNP markers. Muchero et al. [45] also identified three QTL for resistance to Thrips tabaci and Frankliniella schultzei based on an AFLP genetic linkage map. These QTLs were located on linkage groups 5 and 7 accounting for between 9.1% and 32.1% of the phenotypic variance.

3. Conclusions and Future Prospects The ultimate goal of cowpea research is to classify germplasm resources, protect them and improve the yield and quality effectively. Traditional studies are based on phenotypic selection, and are easily affected by environmental or human factors. Research on the genes that controlling cowpea yield and quality from

the DNA level will improve the cowpea yield and quality eventually. As an important means of breeding, DNA molecular markers have demonstrated its unique advantages, and there have been some progress in its application in cowpea genetic breeding. However, there exists some problems and requires a long way to go in this direction. First of all, many researchers have come to a same conclusion: the genetic diversity of cultivated cowpea is very low [12, 15, 22, 23, 46, 47]. The narrow genetic base is one of the major limiting factors for today’s cowpea breeding, and the consequences are decline in vitality and range of variation. Cowpea improvement should partly rely on the diversity of large wild gene pool [48]. In order to improve the potential for high yield, adaptability, disease and insect resistance, a large number of excellent wild germplasm should be collected and applied in cowpea breeding program. In the second place, QTL studies of quantitative traits in cowpea are few, which cannot satisfy the need of breeding. Many important agronomic and economic characters of cowpea such as yield, protein content,

A Review of Molecular Makers Applied in Cowpea (Vigna unguiculata L. Walp.) Breeding

resistance and maturity are complex quantitative traits. Mapping more QTL of quantitative trait, analyzing the linkage between molecular marker and them are significant for research on marker-assisted breeding, mechanism of heterosis, genetic diversity, isolation and clone of quantitative trait gene. Last but not the least, few molecular markers linked to resistance gene have been found. There are a lot of diseases like rust, powdery mildew, fusarium wilt, and insect pests like bean weevil, pod borer in cowpea production. Seeking for more molecular markers linked to disease and insect resistance genes is an important means of assisted selection in breeding. The material could be selected on the DNA level with the help of molecular markers linked to resistance gene, and single or multiple genes linked to target traits could be detected, localized and tracked, thus reducing the blindness of selection and achieving the efficient improvement of cowpea yield, quality and resistance

[4]

[5]

[6]

[7]

[8]

[9]

traits. In a word, studies of molecular markers on cowpea

[10]

are still lacking. Molecular marker could be an auxiliary selection mean for breeding new cultivars or lines, but its application in cowpea is at the stage of exploration. Therefore, it is necessary to deepen the

[11]

research of molecular marker techniques in cowpea breeding.

Acknowledgments

[12]

This work was supported by “Shuang-Zhi Plan” of Sichuan Agricultural University, China. [13]

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