DNA fingerprinting reveals varietal composition of Vietnamese cassava germplasm (Manihot esculenta Crantz) from farmers’ field and genebank collections

Abstract

Key message A molecular analysis using informative SNP markers in 1570 clones of cassava from Vietnam reveals varietal composition from farmers’ field and genebank collections Abstract Cassava is the most important smallholder cash crops in Southeast Asia and is especially used in industrial products. Yet, systematic genetic studies on molecular markers from Vietnamese germplasm have not been considered for breeding and conservation programs. We conducted a molecular analysis of 1570 clones of cassava germplasm from farms across six agro-ecological zones using informative SNP markers. We unraveled the genetic diversity and population structure and provided insights into the value of breeding and conservation programs. Duplicated genotypes comprised 98% of the total sample of the Central Highlands region. Ninety-six SNPs were amplified Central Highlands and South East provinces had the highest allelic richness, covering up to 83% of alleles. The average observed heterozygosity (Ho = 0.43) was slightly higher than expected (He = 0.40) across SNP markers, suggesting an excess of heterozygotes plants. Diversity indexes indicated that cassava populations from North West and Eastern Vietnam are genetically diverse (mean He = 0.40). Genetic parentage tests identified 85 unique genetic groups within the varieties KM94, KM419, BRA1305, KM101, KM140, PER262, KM60, KM57 and two unidentified varieties, which accounted for 82% of the frequency distribution. KM94 is the most dominant variety in Vietnamese farms surveyed (38%), reflecting its superior quality and productivity. Discriminant analysis of principal components (DAPC) revealed four main subgroups, which were partially corroborated by neighbor joining (NJ) analyses. After removing duplicates, 31 unique genotypes were distributed across five of the agro-ecological zones. These were well distributed in the subgroups revealed via DAPC and NJ analyses. The genetic groups identified herein could be used to select unique accessions that should ideally conform with ex situ germplasm collections and identify areas where on-farm conservation programs should be targeted. Newly identified genotypes may also contribute as genetic breeding resources that could be used to adapt cassava to future changes and farmers’ needs.

Identifying New Resistance to Cassava Mosaic Disease and Validating Markers for the CMD2 Locus

“…The pedigree of CIAT102 is available in CassavaBase [23]. The population VNM142 contained 142 clones collected from farms in Vietnam in 2015 [24,25]. From VNM142, we identified 93 unique clones based on the DNA fingerprinting results using a SNP-chip with 96 SNP markers at CIAT (SNPY-Array; Fluidigm ® , South San Francisco, CA, USA) [26,27].…”

Identification of Cassava Varieties in Ex-Situ Collections and Global Farmer’s Fields: An Update from 1990 to 2020

“…These genomic variations were unraveled by re-sequencing using restriction-site associated DNA-sequencing (RAD-seq) [145] or genotyping by sequencing (GBS) [147]. These two methods can detect small genetic differences between individuals, and therefore may be useful for studying organisms with reduced genetic Plant materials used: [1] Collection maintained at CIAT's GRU, [2] Collection maintained at IITA's GRU, [3] Collection maintained at ORSTOM (IRD-France), [4] Field collection in Tanzania and Nigeria, [5] Field collected in Kibaha and Ikiriguru, [6] Collection maintained at National Agricultural Research Institute, Maputo, [7] Field collected in Hoima, Kumi, and Luwero districts, [8] Field collected in Baka, Mkondezi, Chitala, Chitedze, and Makoka Agricultural Research Stations, [9] Collection maintained at Plant Genetic Resource Research Institute at Bunso in the Eastern Region of Ghana and the University of Cape Coast, [10] Collection maintained at MARI, [11] Collection maintained at CSIR-Crops Research Institute (CRI), [12] Collection maintained at Kenya Agricultural Research Institute (KARI), [13] Collection maintained at University of Kinshasa, [14] Collection maintained at CNRA, [15] Field collected in Ghana Brong Ahafo, Ashanti, and Eastern, [16] Field collected in North Central followed by South-South, Southwest, and Southeast regions, [17] Field collected in Southern and Central Benin, [18] Field collected in Apac, Arua, Kibaale, and Masindi, [19] Collection maintained at Njala Agricultural Research Centre (NARC), [20] Collection maintained at ICAR-Central Tuber Crops Research Institute, Sreekariyam, Thiruvanathapuram, [21] Tapioca and Castor Research Station (T&CRS) GRU, [22] Field collected in Campinas, [23] Field collected in Makushi Village, [24] Field Collected in Sao Paolo state, [25] Embrapa Cassava and Fruit Crops, Cruz das Almas, BA, [26] Field collection in Rewa, a Makushi community, …”

“…Since its official release in Thailand, this variety has spread throughout SEA. In Vietnam, KU50 was released in 1995 as KM94, and was later introduced in Cambodia as Malay [12][13][14]. It covers nearly one million hectares today.…”

“…Out of the 50 gene banks surveyed, 34 provided information that allowed the estimation that as many as 14,791 distinct landraces were under conservation in gene banks [18]. The real number, however, is likely be significantly lower, once all varieties are characterized using DNA-based molecular markers [2,4,12].…”

“…In the past 30 years, a body of knowledge about the varietal identification and genetic diversity of cassava has been developed for genetic materials found in ex-situ collections, experimental field trials, and farmers' fields, using morphological descriptors [17,, morphological descriptors and molecular markers [16,[49][50][51][52][53][54][55][56][57], and molecular markers alone [2,4,12,15,25,. The morphological…”