Characterization of Microsatellites in the Akebia trifoliata Genome and Their Transferability and Development of a Whole Set of Effective, Polymorphic, and Physically Mapped Simple Sequence Repeat Markers

Genome-wide development of simple sequence repeats markers and genetic diversity analysis of chayote

BACKGROUND

Chayote is a high economic crop in the Cucurbitaceae family, playing an important role in food production, disease treatment and the production of degradable materials in industries. Due to the harsh environment, such as high temperature, drought and frost, some chayote resources are gradually disappearing. It is crucial to collect, characterize, and conserve chayote resources. However, the genetic diversity of chayote resources in China has not been studied so far.

RESULTS

In this study, we collected 35 individuals of chayote from 14 provinces in China. Subsequently, we found 363,156 SSR motifs from the chayote genome and designed 57 pairs of SSR primers for validation. Out of these, 48 primer pairs successfully amplified bands, with 42 of them showing polymorphism. These 42 primer pairs detected a total of 153 alleles, averaging 3.64 alleles per locus. The polymorphic information content ranged from 0.03 to 0.78, with an average value of 0.41, indicating a high level of polymorphism. Based on the analysis using STRUCTURE, PCoA, and UPGMA methods, the 35 chayote individuals were divided into two major clusters. Through further association analysis, 7 significantly associated SSR markers were identified, including four related to peel color and three related to spine.

CONCLUSIONS

These molecular markers will contribute to the analysis of genetic diversity and genetic breeding improvement of chayote in the future.

Germplasm resources and genetic improvement of Akebia: A new fruit crop in China

Akebia species, belonging to Lardizabalaceae, are widespread from subtropical to temperate environments of China, Japan, and Korea. All known Akebia species have medicinal and dietary value and have been widely cultivated as a new fruit crop in many areas of China. However, compared with other crop species, the breeding improvement and commercial cultivation of Akebia remain in their infancy. This review systematically introduces the present germplasm resources, geographical distribution, biological characteristics, interspecific and intraspecific cross compatibility, molecular biology, and breeding progress in Akebia species. Akebia plants are widely distributed in Shanxi, Henan, Sichuan, Chongqing, Hunan, Hubei, Jiangxi, Zhejiang, and Fujian provinces of China, and wild Akebia plants exhibit abundant phenotypic and genetic diversity due to their wide range of geographical distribution and high adaptability in different habitats. Interspecific artificial hybridization experiments have been conducted in our Akebia germplasm resources nursery. The results showed that there was no reproductive isolation between Akebia species, and fertile progeny could be produced. The synthesis of knowledge on these species provides insights for the rational development and utilization of these germplasm resources, and can facilitate the development of new breeding lines or varieties for commercial cultivation or production. Finally, perspectives on Akebia breeding research are discussed and conclusions are provided. This review provided breeders with new insights into Akebia domestication and breeding, and we also proposed five basic steps in the domestication of new fruit crops.

Expression Profiles of Microsatellites in Fruit Tissues of Akebia trifoliata and Development of Efficient EST-SSR Markers

Akebia trifoliata, a member of the family Lardizabalaceae, has high exploitation potential for multiple economic purposes, so genetic improvements to meet requirements for commercial demand are needed. However, this progress is largely impeded by a lack of effective selection markers. In this study, we obtained 271.49 Gb of clean transcriptomic data from 12 samples (three tissues at four developmental stages) of A. trifoliata fruit. We identified 175,604, 194,370, and 207,906 SSRs from the de novo assembled 416,363, 463,756, and 491,680 unigene sequences obtained from the flesh, seed, and rind tissues, respectively. The profile and proportion of SSR motifs expressed in each fruit tissue and developmental stage were remarkably similar, but many trinucleotide repeats had differential expression levels among different tissues or at different developmental stages. In addition, we successfully designed 16,869 functional EST-SSR primers according to the annotated unigenes. Finally, 94 and 72 primer pairs out of 100 randomly selected primer pairs produced clear bands and polymorphic bands, respectively. These results were also used to elucidate the expression profiles of different tissues at various stages. Additionally, we provided a set of effective, polymorphic, and reliable EST-SSR markers sufficient for accelerating the discovery of metabolic and pathway-specific functional genes for genetic improvement and increased commercial productivity.