Typology of shrimp farming in Bac Lieu Province, Mekong Delta, using multivariate statistics

Joffre, Olivier; Bosma, R.H.

doi:10.1016/j.agee.2009.03.010

Cited by 70 publications

(51 citation statements)

References 12 publications

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Section: Discussionsupporting

confidence: 82%

“…While these factors could explain why more virulent WSSV strains with longer Indel-II deletions and shorter overall genomes (Zwart et al 2010) were found more frequently in semi-intensive ponds systems, no data were collected on the hatchery sources of PL, which might also influence what genotypes were detected. In any case, our data support those of other studies in which farming practices have been found to influence the risk of disease (Joffre & Bosma 2009) and what WSSV genotypes exist in the shrimp (Dieu et al 2011).Examining WSSV Indel-I and Indel-II types in a large number of healthy and diseased shrimp collected over a 3 yr period from various farm types in 2 provinces in the Mekong Delta found that Indel-I types have little epidemiological value, but longer Indel-II deletions correlated significantly with diseased shrimp that were emergency harvested at semi-intensive farms. Editorial responsibility: Jeff Cowley,…”

supporting

confidence: 82%

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Indel-II region deletion sizes in the white spot syndrome virus genome correlate with shrimp disease outbreaks in southern Vietnam

Tuyet¹,

Zwart²,

Phượng³

et al. 2012

Dis. Aquat. Org.

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Sequence comparisons of the genomes of white spot syndrome virus (WSSV) strains have identified regions containing variable-length insertions/deletions (i.e. indels). Indel-I and Indel-II, positioned between open reading frames (ORFs) 14/15 and 23/24, respectively, are the largest and the most variable. Here we examined the nature of these 2 indel regions in 313 WSSVinfected Penaeus monodon shrimp collected between 2006 and 2009 from 76 aquaculture ponds in the Mekong Delta region of Vietnam. In the Indel-I region, 2 WSSV genotypes with deletions of either 5950 or 6031 bp in length compared with that of a reference strain from Thailand (WSSV-TH-96-II) were detected. In the Indel-II region, 4 WSSV genotypes with deletions of 8539, 10 970, 11 049 or 11 866 bp in length compared with that of a reference strain from Taiwan (WSSV-TW) were detected, and the 8539 and 10 970 bp genotypes predominated. Indel-II variants with longer deletions were found to correlate statistically with WSSV-diseased shrimp originating from more intensive farming systems. Like Indel-I lengths, Indel-II lengths also varied based on the Mekong Delta province from which farmed shrimp were collected.KEY WORDS: White spot syndrome virus · Disease status · Farming system · Epidemiology · ORF 14/15 · ORF 23/24Resale or republication not permitted without written consent of the publisher Dis Aquat Org 99: [153][154][155][156][157][158][159][160][161][162] 2012 highly (> 99.5%) conserved (Nadala & Loh 1998, Marks et al. 2004.The 2 major genomic indels are located between open reading frames (ORFs) 14/15 (Indel-I) and 23/24 (Indel-II) of the sequenced Thai strain WSSV-TH-96-I (van Hulten et al. 2001, Marks et al. 2004. Compared with another sequenced Thai strain (WSSV-TH-96-II), WSSV-TH-96-I has a 5.3 kb deletion in Indel-I (Marks et al. 2005) and differs from a strain from Taiwan (WSSV-TW) by possessing a 13.2 kb deletion in Indel-II (Marks et al. 2004). Sequence analyses of these 2 indel regions in other Asian WSSV strains have identified intermediatelength deletions (Dieu et al. 2004, Zwart et al. 2010. For example, WSSV strains from China contain shorter Indel-II deletions (1168 to 5928 bp) compared with WSSV-TW, while strains from Vietnam contain a medium-length Indel-II deletion (~8539 bp) not yet found in strains examined from other geographic regions (Dieu et al. 2004; see also Yang et al. 2001, Lan et al. 2002, Tan & Shi 2011.Indel-I and Indel-II regions are now being used as molecular markers to study WSSV epidemiology (Dieu et al. 2004, Zwart et al. 2010, and Indel-II is proving to be particularly useful for examining the spatiotemporal spread of WSSV at regional (Dieu et al. 2010) and intercontinental levels (Zwart et al. 2010). Data on Indel-II support a hypothesis that all WSSV strains affecting farmed shrimp have a recent common ancestor. This virus presumably circulated in China or Taiwan before spreading to shrimp farms in Vietnam, from there to Thailand (Dieu et al. 2004) and from there to India (Pradeep et al. 2008a)...

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Section: Discussionsupporting

confidence: 82%

supporting

confidence: 82%

Indel-II region deletion sizes in the white spot syndrome virus genome correlate with shrimp disease outbreaks in southern Vietnam

Tuyet¹,

Zwart²,

Phượng³

et al. 2012

Dis. Aquat. Org.

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“…PCA and CA have been used to identify farm types worldwide (Bidogeza, Berentsen, De Graaff, & Oude Lansink, 2009;Gebauer, 1987;Joffre & Bosma, 2009;Köbrich, Rehman, & Khan, 2003;Kostov & McErlean, 2006;Maseda, Dıaz, & Alvarez, 2004;SiegmundSchultze & Rischkowsky, 2001;Somda, Kamuanga, & Tollens, 2005). However, although commonly used, these techniques are often not the most appropriate methods in a good number of farming systems studies.…”

Section: Multivariate Approaches For Classificationmentioning

confidence: 98%

Exploring the diversity of urban and peri-urban agricultural systems in Sudano-Sahelian West Africa: An attempt towards a regional typology

Dossa

Abdulkadir

Amadou

et al. 2011

Landscape and Urban Planning

108

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“…Even though, the numbers presented in Table 4.2 can only be taken as broad proxy values due to the signi fi cant complexity and variability for speci fi c production modes, locations and times of assessment, they hint towards considerable economic and social challenges (Nhan 2009 ;Joffre and Bosma 2009 ) . The combination of land conversion with a reduction in labour demand generates a shortage of employment opportunities for the rural work force, notably for those farmers who lost their land (see below).…”

Section: Agricultural Transformationmentioning

confidence: 99%

The Mekong Delta System

Renaud¹,

Kuenzer²

2012

Springer Environmental Science and Engineering

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Typology of shrimp farming in Bac Lieu Province, Mekong Delta, using multivariate statistics

Cited by 70 publications

References 12 publications

Indel-II region deletion sizes in the white spot syndrome virus genome correlate with shrimp disease outbreaks in southern Vietnam

Indel-II region deletion sizes in the white spot syndrome virus genome correlate with shrimp disease outbreaks in southern Vietnam

Exploring the diversity of urban and peri-urban agricultural systems in Sudano-Sahelian West Africa: An attempt towards a regional typology

The Mekong Delta System

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