Bitter gourd is a common, annual, climbing herbaceous medicinal plant, and a melon vegetable suitable for cultivation in temperate and tropical regions. Bitter gourd originated in tropical Africa [1] and is mainly distributed in tropical and subtropical regions of Asia and Africa, as well as in the Amazon region of Brazil, the Caribbean, and South Africa [2, 3].
Several wild bitter gourd genetic resources have been found in the southern foothills of the Himalayas. Particularly, India is home to some of the wildest bitter gourd germplasm, followed by Southeast Asian countries, such as Thailand and Myanmar, and the Yunnan and Hainan areas in China[4]. Wild bitter gourd fruit is small, thin, and prickly; furthermore, because of its strong bitter taste, it is difficult to eat but after years of domestication, modern cultivated bitter gourd varieties have developed thick and long flesh, an increased weight, and a milder bitter taste and are more suitable for eating. Expanding research efforts have confirmed a high nutritional value and medicinal potential of bitter gourd for reducing blood glucose levels in patients with diabetes [5] .
Genetic resources provide abundant genetic variation for cultivar improvement as well as genetic and biological research. Germplasm is an important part of genetic diversity, the basic premise of agricultural origin and development, and the raw material for various breeding pathways, which largely determine the breeding effect [6]. As in any other horticultural crop, any major breakthrough in bitter gourd breeding depends on the development and utilization of key germplasm. Breeding high-quality bitter gourd varieties requires access to extensive genetic resources. In addition, genetic diversity and genetic relationship analysis are the main concerns while evaluating germplasm resources. Genetic diversity is a reflection of plant adaptability to environmental changes, which in turn is reflected at the morphological, cytological, physiological, and biochemical levels [7].
Analysis of genetic diversity and genetic relationship of agronomic traits within a germplasm sample is of great significance for the development and utilization of germplasm resources. Thus, for example, Huang et al. [8] used 28 morphological traits to conduct cluster analysis of 33 bitter gourd accessions, and divided them into three groups, namely, a wildtype group, a dense tumor, small-fruit type group and a long-fruit type group. They found that there were obvious regional differences among groups. Further, the genetic distance between Chinese bitter gourd germplasm and germplasm resources from India and Southeast Asia was relatively large. Some bitter gourd varieties reflect differences in morphological characteristics that are quite different from the classification of morphological experience.
More recently, Kang et al. [9] used ISSR molecular markers to study the genetic diversity among 48 bitter gourd samples. They found that Jiangxi variety 608 and Fujian variety 615 were similar in skin maturity, color, and shape but the characteristics of the fruit surface differed. Similarly, Dhillon et al. [10] used 50 pairs of SSR primers to conduct cluster analysis on 114 bitter gourd accessions from Asia. The genetic similarity coefficients ranged between 0.61 and 0.88, and they were divided into four groups at a threshold value of 0.66. Further, Wang [11] used morphological markers and SRAP and SSR molecular markers to conduct cluster analysis on 14 accessions of Momordica charantia. He found that the similarity of clustering based on morphological markers and molecular markers reached 78.57%; furthermore, the genetic differences among the 14 accessions were not significant. However, the clustering results obtained based on the two molecular markers were very close, indicating that molecular marker-based clustering might be more reliable. Therefore, it is better to study the diversity among germplasm accessions using molecular markers than using morphological characteristics, as the former can accurately indicate the genetic relationship of bitter gourd at the molecular level and determine the extent of homology.
Some varieties with similar morphological characteristics can be clustered together, thus confirming the correctness of the traditional morphological classification framework, which can be supplemented and refined by clustering agronomic traits based on differences at the DNA level. Therefore, the evaluation, innovation, and utilization of molecular markers within bitter gourd germplasm certainly warrants further support.
Insertion-deletion length polymorphism (InDel) refers to the difference between two materials relative to the whole species genome. Compared with each other, there will much likely be a certain number of nucleotide insertions or deletions in the genome of one material which do not exist in the other. As a new generation of markers, InDel markers are widely distributed, numerous, highly polymorphic, stable in variation, low in price, and co-dominant in the genome of a species. To date, InDel markers have been successfully applied to the study of rice, cucumber, and pepper germplasm, among other crops. For example, Hayashi et al. [12] developed a set of InDel markers for the blast-resistance gene in rice. In turn, Li et al. [13] explored InDel loci based on re-sequencing results and used 134 pairs of InDel primers to detect the effectiveness of 16 typical cucumber genotypes. Their results showed that 116 pairs of InDel primers fully revealed the diversity and specificity of the 16 genotypes. Similarly, Li et al. [14] developed InDel markers for pepper genetic mapping using two inbred lines, BA3 and B702, with genome-wide re-sequencing; they obtained a linkage genetic map based on the InDel markers developed, which consisted of 12 linkage groups with a genetic distance of 1178.01 cM and an average distance of 5.01 cM between bin markers.
With the release of the bitter gourd genome, SSR markers [15] and InDel markers [16] have been developed for the whole species genome. However, InDel markers have not been reported for genetic diversity analysis of bitter gourd germplasm. According to the whole genome series of bitter gourd Dali-11, two materials, namely, No. 12 from Guangxi and H-13 from Guangdong were re-sequenced to develop InDel markers. The fruits of these two materials are green and straight tumor, but their sources and fruit lengths are different. The fruit of No. 12 is longer (35–40 cm) and shows late maturity, while the fruit of H-13 is shorter (approximately 20 cm) and shows early maturity. There is strong heterosis between the two materials, which is important to re-sequence and develop InDel markers. Concomitantly, this set of markers was used to screen out the core markers to construct the molecular fingerprints of 53 bitter gourd germplasm accessions from different regions in China, as well as other countries, which can be used for variety identification and for determination of hybrid seed purity. Finally, the genetic relationship of the tested materials was analyzed to provide a theoretical reference for the selection of parents in the process of breeding superior varieties.