Development of high‐resolution DNA barcodes for <i>Dioscorea</i> species discrimination and phylogenetic analysis

Xia, Wei; Zhang, Bo; Xing, Dan; Liu, Ying; Wu, Wen-Qiang; Xiao, Yong; Sun, Jun; Dou, Yajing; Tang, Wenqi; Zhang, Jinlan; Huang, Xiaolong; Xu, Yun; Xie, Jun; Wang, Jihua; Huang, Dong

doi:10.1002/ece3.5605

Cited by 16 publications

(10 citation statements)

References 36 publications

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“…In addition, no gene arrangements were detected either within D. alata or in comparison to its closely related species (i.e., D. brevipetiolata , D. cirrhosa , D. glabra , D. japonica, and D. polystachya ) ( Figure 2 ). These findings were also largely consistent with the characteristics of previously published plastomes of Dioscorea , which showed that the plastomes in this genus were well-conserved [ 29 , 30 , 31 ].…”

Section: Discussionsupporting

confidence: 91%

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: Discussionsupporting

confidence: 91%

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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“…The same trend was observed on SPE as the highest values were on D. rotundata × D. burkilliana cross-combinations. This relatively higher cross-compatibility rate could be attributed to high genetic relatedness among these species, as reported by previous studies 22 , 25 , 29 – 31 . However, interspecific crosses involving D. rotundata with D. cayenensis had generally low success rates due to expected differences in ploidy level.…”

Section: Discussionsupporting

confidence: 76%

Cross compatibility in intraspecific and interspecific hybridization in yam (Dioscorea spp.)

Mondo

Agre

Edemodu

et al. 2022

Sci Rep

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Yam (Dioscorea spp.) is a staple crop for millions of people in the tropics and subtropics. Its genetic improvement through breeding is being challenged by pre-zygotic and post-zygotic cross-compatibility barriers within and among species. Studies dissecting hybridization barriers on yam for improving the crossability rates are limited. This study aimed to assess the cross-compatibility, which yielded fruit set, viable seeds and progeny plants in an extensive intraspecific and interspecific crossing combinations in a yam genetic improvement effort to understand the internal and exogenous factors influencing pollination success. Cross-compatability was analyzed at the individual genotype or family level using historical data from crossing blocks and seedling nurseries from 2010 to 2020 at the International Institute of Tropical Agriculture (IITA). The average crossability rate (ACR) was lower in interspecific crossing combinations (6.1%) than intraspecific ones (27.6%). The seed production efficiency (SPE) values were 1.1 and 9.3% for interspecific and intraspecific crosses, respectively. Weather conditions and pollinator's skills are the main contributors to the low success rate in the intraspecific cross combinations in yam breeding. At the same time, genetic distance and heterozygosity played little role. Interspecific cross barriers were both pre-zygotic and post-zygotic, resulting from the evolutionary divergence among the yam species. Dioscorea rotundata had higher interspecific cross-compatibility indices than D. alata. Distant parents produced intraspecific crossbred seeds with higher germination rates compared to closest parents (r = 0.21, p = 0.033). This work provided important insights into interspecific and intraspecific cross-compatibility in yam and suggested actions for improving hybridization practices in yam breeding programs.

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“…Three plastid loci usually showing high polymorphism and commonly used for DNA barcoding (e.g., Hollingsworth et al, 2011;Xia et al, 2019) were tested for amplification and sequencing. The plastid marker rps16 (with rpsF and rpsR2; Oxelman et al, 1997) did not amplify.…”

Section: Plastid Dna Sequencingmentioning

confidence: 99%

Assessing Population Genetic Status for Designing Plant Translocations

Rossum

Pajolec

Raspé

et al. 2022

Front. Conserv. Sci.

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Assisted gene flow interventions such as plant translocations are valuable complementary techniques to habitat restoration. Bringing new genetic variants can contribute to increasing genetic diversity and evolutionary resilience, counteract inbreeding depression and improve plant fitness through heterosis. Large, highly genetically variable populations are usually recommended as sources for translocation. Unfortunately, many critically endangered species only occur as small populations, which are expected to show low genetic variation, high inbreeding level, paucity of compatible mates in self-incompatible species, and increased genetic divergence. Therefore, assessment of population genetic status is required for an appropriate choice of the source populations. In this paper, we exemplify the different analyses relevant for genetic evaluation of populations combining both molecular (plastid and nuclear) markers and fitness-related quantitative traits. We assessed the genetic status of the adult generation and their seed progeny (the potential translocation founders) of small populations of Campanula glomerata (Campanulaceae), a self-incompatible insect-pollinated herbaceous species critically endangered in Belgium. Only a few small populations remain, so that the species has been part of a restoration project of calcareous grasslands implementing plant translocations. In particular, we estimated genetic diversity, inbreeding levels, genetic structure in adults and their seed progeny, recent bottlenecks, clonal extent in adults, contemporary gene flow, effective population size (Ne), and parentage, sibship and seed progeny fitness variation. Small populations of C. glomerata presented high genetic diversity, and extensive contemporary pollen flow within populations, with multiple parentage among seed progenies, and so could be good seed source candidates for translocations. As populations are differentiated from each other, mixing the sources will not only optimize the number of variants and of compatible mates in translocated populations, but also representativeness of species regional genetic diversity. Genetic diversity is no immediate threat to population persistence, but small Ne, restricted among-population gene flow, and evidence of processes leading to genetic erosion, inbreeding and inbreeding depression in the seed progeny require management measures to counteract these trends and stochastic vulnerability. Habitat restoration facilitating recruitment, flowering and pollination, reconnecting populations by biological corridors or stepping stones, and creating new populations through translocations in protected areas are particularly recommended.

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Development of high‐resolution DNA barcodes for Dioscorea species discrimination and phylogenetic analysis

Cited by 16 publications

References 36 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

Cross compatibility in intraspecific and interspecific hybridization in yam (Dioscorea spp.)

Assessing Population Genetic Status for Designing Plant Translocations

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