Development and use of microsatellite markers for genetic diversity analysis of cañahua (Chenopodium pallidicaule Aellen)

Vargas, A.; Elzinga, Dave B.; Rojas-Beltran, J.; Bonifacio, Alejandro; Geary, Brad; Stevens, Mikel R.; Jellen, Eric N.; Maughan, Peter J.

doi:10.1007/s10722-010-9615-z

Cited by 11 publications

(10 citation statements)

References 33 publications

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“…This finding agrees with those of Vargas et al. () and is further evidence that the wild accessions may be useful sources of novel genetic diversity for improving cañahua.…”

Section: Resultssupporting

confidence: 93%

“…Ruas et al (1999) published a phylogenetic study of 19 Chenopodium L. species based on RAPD markers, including two cañahua accessions that were found to be nearly identical. Vargas et al (2011) developed the first microsatellite markers for cañahua, including 34 polymorphic markers, exhibiting a total of 154 different alleles. A phylogeny of 43 cañahua accessions showed clear distinctions between wild and cultivated lines, including a distinct subclade of erect morphotypes.…”

Section: Of 12mentioning

confidence: 99%

“…Vargas et al. () developed the first microsatellite markers for cañahua, including 34 polymorphic markers, exhibiting a total of 154 different alleles. A phylogeny of 43 cañahua accessions showed clear distinctions between wild and cultivated lines, including a distinct subclade of erect morphotypes.…”

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confidence: 99%

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The genome of Chenopodium pallidicaule: An emerging Andean super grain

et al. 2019

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Premise Cañahua is a semi‐domesticated crop grown in high‐altitude regions of the Andes. It is an A‐genome diploid (2n = 2x = 18) relative of the allotetraploid (AABB) Chenopodium quinoa and shares many of its nutritional benefits. Cañahua seed contains a complete protein, a low glycemic index, and offers a wide variety of nutritionally important vitamins and minerals. Methods The reference assembly was developed using a combination of short‐ and long‐read sequencing techniques, including multiple rounds of Hi‐C–based proximity‐guided assembly. Results The final assembly of the ~363‐Mbp genome consists of 4633 scaffolds, with 96.6% of the assembly contained in nine scaffolds representing the nine haploid chromosomes of the species. Repetitive element analysis classified 52.3% of the assembly as repetitive, with the most common repeat identified as long terminal repeat retrotransposons. MAKER annotation of the final assembly yielded 22,832 putative gene models. Discussion When compared with quinoa, strong patterns of synteny support the hypothesis that cañahua is a close A‐genome diploid relative, and thus potentially a simplified model diploid species for genetic analysis and improvement of quinoa. Resequencing and phylogenetic analysis of a diversity panel of cañahua accessions suggests that coordinated efforts are needed to enhance genetic diversity conservation within ex situ germplasm collections.

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“…This finding agrees with those of Vargas et al. () and is further evidence that the wild accessions may be useful sources of novel genetic diversity for improving cañahua.…”

Section: Resultssupporting

confidence: 93%

Section: Of 12mentioning

confidence: 99%

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The genome of Chenopodium pallidicaule: An emerging Andean super grain

et al. 2019

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“…Different varieties of quinoa are adapted to a range of growing conditions and display diverse grain colours, shapes, inflorescence sizes, and seed characteristics (Del Castillo et al 2008;Bazile et al 2013). Cañahua, oca, papalisa, and isaño also exhibit high intraspecific variation (Malice and Baudoin 2009;Vargas et al 2011;Velasquez-Milla et al 2011;Mutegi et al 2015). Because of this exceptional diversity, the Andean highlands-and notably the Lake Titicaca region-are recognized as a centre of globally important crop genetic resources (Garcia et al 2007;Velasquez-Milla et al 2011).…”

Section: Introductionmentioning

confidence: 99%

Climate change and crop diversity: farmers’ perceptions and adaptation on the Bolivian Altiplano

Meldrum

Mijatović²,

Rojas

et al. 2017

Environ Dev Sustain

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Crop diversity is central to traditional risk management practices on the Andean Altiplano and may find renewed importance in adapting to climate change. This study explored the role of crop diversity in farmers' adaptation actions in eight Aymara communities on the northern Bolivian Altiplano. Using a combination of quantitative and qualitative methods, including multifactor analysis and a community resilience selfassessment, we investigated how farmers' use of diversity in adaptation is related to their perceptions of crop and variety tolerances and other environmental, social, and economic factors. Few crops and varieties were perceived as tolerant to increasingly intense and unpredictable drought, frost, hail, and pest and disease outbreaks. Some local crops and varieties were perceived as vulnerable to emerging conditions (e.g. oca, papalisa, isaño), whereas bitter potatoes and wild relatives of quinoa and cañahua were perceived as highly stress tolerant and provide food in harsh periods. A total 19% of households surveyed (N = 193) had introduced new crops or varieties-often disease resistant or early maturing-as an adaptive action. Introduction of commercial crops was a common adaptation action, reflecting farmers' response to warming temperatures and changing economic opportunities, but greater sensitivity of the introduced crops may cause maladaptation. Despite intensification of cropping systems, households continue to maintain a median four potato varieties with different tolerance traits, yet this risk management practice was not perceived as adaptation. Strengthening resilience will require a combination of actions, including maintaining and expanding crop portfolios and restoring soil and ecosystem health, using both traditional and innovative approaches.

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“…Among molecular markers, those most frequently used for genotyping were simple sequence repeats (SSRs) (Tautz, 1989). Several studies described the use of SSRs to reveal polymorphism in the Andean pseudocereals amaranth (Mallory et al, 2008), kanihua (Vargas et al, 2011), and quinoa (Fuentes et al, 2009; Jarvis et al, 2008; Mason et al, 2005; Maughan et al, 2004; Pissard et al, 2006). The primary drawbacks of SSR markers are that they may be difficult to score manually and they are relatively expensive for high‐throughput genotyping applications.…”

mentioning

confidence: 99%

Assessment of Genetic Diversity in Peruvian Amaranth (Amaranthus caudatus and A. hybridus) Germplasm using Single Nucleotide Polymorphism Markers

et al. 2013

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Amaranth (Amaranthus caudatus L.) is an important seed crop in the Andes. It has excellent nutritional value and ample capacity for growth under drought, heat, and soil nutrient deficiency. The objective of this study was to characterize and quantify genetic diversity among a series of 178 mostly Peruvian amaranth individuals genotyped from among 48 accessions using 96 biallelic single nucleotide polymorphism (SNP) markers in KASPar assays on a 96.96 Fluidigm EP1 platform. The 178 seed genotypes included the predominant white‐opaque (waxy), white‐vitreous (nonwaxy), black, and brown types, all from within the Centro de Investigacion de Cultivos Andinos‐Universidad Nacional de San Antonio Abad del Cusco collection. The samples separated into two groups based on the seed color parameter (black, brown, and white‐vitreous versus white‐opaque) with STRUCTURE analysis but did not form distinct genotypic groups based on geographic origin. When analyzed as seed‐color subgroups—black vs. brown vs. white‐vitreous vs. white‐opaque—83.46% of the genetic variation was explained by genetic differences within subgroup. The highest average observed heterozygosity (Ho) within color‐based subgroups was 0.2612 in the vitreous‐seeded subgroup, and within‐group expected heterozygosity (He) was highest in the brown‐seeded subgroup (0.398). Cluster analysis and principal component analysis partitioned the amaranth accessions into two clusters with four distinct subclusters. Analyses also revealed evidence for selection of nonwaxy, vitreous‐seeded amaranth in the Andes.

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Development and use of microsatellite markers for genetic diversity analysis of cañahua (Chenopodium pallidicaule Aellen)

Cited by 11 publications

References 33 publications

The genome of Chenopodium pallidicaule: An emerging Andean super grain

The genome of Chenopodium pallidicaule: An emerging Andean super grain

Climate change and crop diversity: farmers’ perceptions and adaptation on the Bolivian Altiplano

Assessment of Genetic Diversity in Peruvian Amaranth (Amaranthus caudatus and A. hybridus) Germplasm using Single Nucleotide Polymorphism Markers

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