Characterizing diversity based on phenotypes and molecular marker analyses of purple yam (Dioscorea alata L.) germplasm in southern China

Chen, Xin; Sun, Jingyu; Zhu, Qianglong; Xiao, Yao; Zhang, Hongyu; Huang, Yongji; Wang, Putao; Cao, Tianxu; Hu, Rui; Xiang, Zijin; Shan, Nan; Zhou, Qinghong

doi:10.1007/s10722-022-01388-5

Cited by 5 publications

(8 citation statements)

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“…According to our field observation and previous phenotype- and SSR-based studies [ 12 , 16 ], a total of 44 accessions ( Table 1 ) representing the major cultivars of D. alata in China were selected for whole genome sequencing. These accessions, with high phenotypic diversity, covered the main distribution area of this species in China, from west (Lijiang, Yunnan Province, geographic coordinates (gc): 26°43′ N, 100°15′ E) to east (Taizhou, Zhejiang Province, gc: 28°38′ N, 121°27′ E), and from south (Sanya, Hainan Province, gc: 18°24′ N, 109°45′ E) to north (Xuzhou, Jiangsu Province, gc: 34°39′ N, 116°35′ E).…”

Section: Methodsmentioning

confidence: 99%

“…To date, however, genetic variations of Chinese D. alata accessions remain ambiguous, although several simple sequence repeat (SSR)-based studies have been conducted. For example, Wu et al [ 12 ] divided Chinese accessions of D. alata into two major clades, based on the unweighted pair-group method with arithmetic mean (UPGMA) and principal coordinate analysis (PCA), while Chen et al [ 16 ] revealed the existence of three sub-populations in Chinese accessions based on a model-based population structure analysis. Thus, resolving genetic variations in Chinese D. alata accessions is an essential step toward the molecular breeding of this economically significant species in China.…”

Section: Introductionmentioning

confidence: 99%

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Pan-Plastome of Greater Yam (Dioscorea alata) in China: Intraspecific Genetic Variation, Comparative Genomics, and Phylogenetic Analyses

Zhang

et al. 2023

IJMS

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Dioscorea alata L. (Dioscoreaceae), commonly known as greater yam, water yam, or winged yam, is a popular tuber vegetable/food crop worldwide, with nutritional, health, and economical importance. China is an important domestication center of D. alata, and hundreds of cultivars (accessions) have been established. However, genetic variations among Chinese accessions remain ambiguous, and genomic resources currently available for the molecular breeding of this species in China are very scarce. In this study, we generated the first pan-plastome of D. alata, based on 44 Chinese accessions and 8 African accessions, and investigated the genetic variations, plastome evolution, and phylogenetic relationships within D. alata and among members of the section Enantiophyllum. The D. alata pan-plastome encoded 113 unique genes and ranged in size from 153,114 to 153,161 bp. A total of four whole-plastome haplotypes (Haps I–IV) were identified in the Chinese accessions, showing no geographical differentiation, while all eight African accessions shared the same whole-plastome haplotype (Hap I). Comparative genomic analyses revealed that all four whole plastome haplotypes harbored identical GC content, gene content, gene order, and IR/SC boundary structures, which were also highly congruent with other species of Enantiophyllum. In addition, four highly divergent regions, i.e., trnC–petN, trnL–rpl32, ndhD–ccsA, and exon 3 of clpP, were identified as potential DNA barcodes. Phylogenetic analyses clearly separated all the D. alata accessions into four distinct clades corresponding to the four haplotypes, and strongly supported that D. alata was more closely related to D. brevipetiolata and D. glabra than D. cirrhosa, D. japonica, and D. polystachya. Overall, these results not only revealed the genetic variations among Chinese D. alata accessions, but also provided the necessary groundwork for molecular-assisted breeding and industrial utilization of this species.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Pan-Plastome of Greater Yam (Dioscorea alata) in China: Intraspecific Genetic Variation, Comparative Genomics, and Phylogenetic Analyses

Zhang

et al. 2023

IJMS

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“…27,28 Purple yam is enriched in anthocyanins, which are strong antioxidants providing additional nutritional value. 41 As yam is widely consumed in West Africa, developing nutritionally enhanced cultivars would have a positive and significant impact on the diet of a large population. Therefore, increasing colorless anthocyanins in yam in order to maintain the desired white FC could be investigated.…”

Section: Discussionmentioning

confidence: 99%

“…Several studies have reported significant variations in the nutritional properties of different colored yams 27,28 . Purple yam is enriched in anthocyanins, which are strong antioxidants providing additional nutritional value 41 . As yam is widely consumed in West Africa, developing nutritionally enhanced cultivars would have a positive and significant impact on the diet of a large population.…”

Section: Discussionmentioning

confidence: 99%

Genome‐wide association studies reveal novel loci controlling tuber flesh color and oxidative browning in Dioscorea alata

et al. 2023

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BACKGROUNDConsumers' preferences for food crops are guided by quality attributes. This study aimed at deciphering the genetic basis of quality traits, especially tuber flesh color (FC) and oxidative browning (OB) in Dioscorea alata, based on the genome‐wide association studies (GWAS) approach. The D. alata panel was planted at two locations in Guadeloupe. At harvest, the FC was scored visually as white, cream, or purple on longitudinally sliced mature tubers. The OB was scored visually as the presence or absence of browning after 15 min of exposure of the sliced samples to ambient air.RESULTSPhenotypic characterization for FC and OB of a diverse panel of D. alata genotypes highlighted significant variation within the panel and across two locations. The genotypes within the panel displayed a weak structure and could be classified into three subpopulations. GWAS identified 14 and 4 significant associations for tuber FC and OB, respectively, with phenotypic variance, explained values ranging from 7.18% to 18.04%. Allele segregation analysis at the significantly associated loci highlighted the favorable alleles for the desired traits, i.e., white FC and no OB. A total of 24 putative candidate genes were identified around the significant signals. A comparative analysis with previously reported quantitative trait loci indicated that numerous genomic regions control these traits in D. alata.CONCLUSIONOur study provides important insights into the genetic control of tuber FC and OB in D. alata. The major and stable loci can be further utilized to improve selection in breeding programs for developing new cultivars with enhanced tuber quality. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

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“…The markers commonly used in morphological characterization of different species of the genus Dioscorea are shape, color, length, and width of the leaf; the presence of wings; the color of the peel and of the pulp; and tuber weight (Wu et al 2019;Cao et al 2021;Chen et al 2022).…”

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confidence: 99%

Genetic diversity of yam (Dioscorea sp.) through morphological and molecular markers

Santos,

Gois,

Prata

et al. 2024

Preprint

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The aim of the present study was to evaluate the genetic diversity of genotypes of Dioscorea sp. originating from states of the Brazilian Northeast region (Sergipe, Bahia, Alagoas, and Paraíba) through morphological and molecular characterization. For this evaluation, 52 yam genotypes were collected from market locations and directly from rural growers. Morphological characterization made use of 31 morphological descriptors for the yam crop. The environmental coefficient of variation (CVe) of most of the descriptors evaluated was greater than the genotypic coefficient of variation (CVg), and heritability was high only for stem color (86.86%). The highest significant positive correlation was between the presence of the tuber and the presence of roots on the surface of the tuber (r = 1; p < 0.001). The genotypes were clustered in seven different groups based on the morphological descriptors evaluated. For molecular characterization, SSR (9) and ISSR (16) primers were used. The primers used were considered informative, showing high polymorphic information content; and 100% of the bands were polymorphic. Genetic diversity was estimated by the following parameters: number of alleles (2.00), effective number of alleles (1.30), expected heterozygosity (0.211), and the Shannon index (0.351). The 52 genotypes were clustered in seven groups according to the Jaccard distance. The genetic structure of the population in K = 2 reveals shared alleles among the genotypes of different geographic origins. Morphological and molecular characterization reveals the high genetic diversity among the 52 genotypes of Dioscorea sp. and low diversity among the collection sites.

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Characterizing diversity based on phenotypes and molecular marker analyses of purple yam (Dioscorea alata L.) germplasm in southern China

Cited by 5 publications

References 27 publications

Pan-Plastome of Greater Yam (Dioscorea alata) in China: Intraspecific Genetic Variation, Comparative Genomics, and Phylogenetic Analyses

Pan-Plastome of Greater Yam (Dioscorea alata) in China: Intraspecific Genetic Variation, Comparative Genomics, and Phylogenetic Analyses

Genome‐wide association studies reveal novel loci controlling tuber flesh color and oxidative browning in Dioscorea alata

Genetic diversity of yam (Dioscorea sp.) through morphological and molecular markers

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