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Phenotypic characteristics of purple yam. The morphology of leaf shape with sagittate and ovate (A), stem wing color are red purple (B), different types of flesh color (C) and tuber skin color (D) were analyzed respectively. Bars of (A), (B), (C) and (D) are 4 cm, 1 cm, 4 cm and 4 cm respectively
Source publication
Purple yam (Dioscorea alata L.), which is widely distributed in southern China, is characterized by great purple to red flesh or skin, as well as nutritional and medical values. However, their intraspecific genetic diversity remains unknown, which inhibits the germplasm innovation and variety protection of purple yams. In this study, genetic divers...
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Background
Characterization and evaluation of plant genetic resources play an important role for their utilization in the crop improvement programmes.
Methods and results
This study involves the agro-morphological and cooking quality besides, molecular characterization of 51 genotypes/advance breeding lines of rice from Kashmir Himalayas. Signific...
Citations
... 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. ...
BACKGROUND
Consumers' 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.
RESULTS
Phenotypic 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.
CONCLUSION
Our 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.
... Different number of effective alleles were reported in previous studies. Chen et al. [17] reported 2.26 effective number of alleles using nine SSR markers in 26 D. alata germplasm from Southern China while Mulualem et al. [35] reported 1.71 effective number of alleles using 10 SSR markers in 33 yam accessions collected from Ethiopia. Generally, the differences in the number of effective alleles can reflect the genetic diversity of the population. ...
Water yam (Dioscorea alata L.) is among the most cultivated species used as a source of food and income for small-scale farmers in Tanzania. However, little is documented about Dioscorea species available in Tanzania, including their genetic diversity. This study used ten polymorphic microsatellite markers to determine the genetic diversity and relationship of 63 D. alata accessions from six major producing regions. Results revealed a polymorphic information content (PIC) of 0.63, while the number of alleles per locus ranged from 4 to 12 with a mean of 7.60. The expected heterozygosity ranged from 0.20to 0.76, with a mean of 0.53, which suggests moderate genetic diversity of D. alata accessions. Kagera region had the highest mean number of (1.5) private alleles. Analysis of molecular variance revealed that 54% of the variation was attributed to within individual, 39% was attributed to among individual while among population contributed 7% of the total variation. The highest Nei's genetic distance (0.43) was for accessions sampled from Kilimanjaro and Mtwara regions. Principal coordinate analysis and cluster analysis using Unweighted Paired Group Method using Arithmetic (UPGMA) grouped D. alata accessions into two major clusters regardless of geographical origin and local names. The Bayesian structure analysis confirmed the two clusters obtained in UPGMA and revealed an admixture of D. alata accessions in all six regions suggesting farmers' extensive exchange of planting materials. These results are helpful in the selection of D. alata accessions for breeding programs in Tanzania.
... 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 pairgroup 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. ...
... 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′), and from south (Sanya, Hainan Province, gc: 18°24′ N, 109°45′ E) to north (Xuzhou, Jiangsu Province, gc: 34°39′ N, 116°35′). ...
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.
