Recent advances in research on the molecular markers, genetic map and QTL mapping in kiwifruit

Abstract: As one of the four most successful fruit crops domesticated from the wild in the 20th century, the kiwifruit accounts for an important place in the development of the fruit industry. It is an ancient plant and also an emerging fruit, and is often referred to as the“king of fruits”due to its rich vitamin content and unique taste. There are 54 species and 21 varieties of the Actinidia Lindl., and they are wide-ly distributed throughout the world. China is the origin of the Actinidia, so our country has rich germ- plasm resources. The Actinidia is characterized as a dioecious plant with a long juvenile period, result-ing in long and inefficient breeding cycle. Since hybrid breeding can achieve combination of superior traits, the breeding route for the Actinidia is increasingly shifting from traditional selection directly from the wild to hybrid breeding. The selection of superior genotypes from the hybrid offspring is the most critical step in the hybrid breeding process. The traditional method mainly relies on phenotypic se-lection for targeted traits. It is time-consuming and difficult, which usually takes 10-15 years to develop a new cultivar. Most phenotypic traits are quantitative traits, which are susceptible to environmental in-fluences and unstable in performance, thus reducing the accuracy of phenotypic selection. With the de-velopment of PCR technology and modern sequencing techniques, marker- assisted selection (MAS)breeding techniques have emerged, which can greatly reduce breeding period and improve breeding ac-curacy as the trait selections are based on genotypes rather than phenotypes. Molecular marker technolo-gy is based on individual nucleotide sequence variation, which is a direct reflection of individual genet-ic variation, allowing differences between organisms to be detected at the nucleotide sequence level. It  has many advantages over traditional morphological and cytological markers: it is not affected by cli- mate or environment, it can be detected in all tissues and organs of plants and at all stages of develop-ment, and it is highly polymorphic. With advances in modern biotechnology, the construction of a genet-ic map is improved from a low-density genetic map constructed by morphological, physiological and biochemical markers to a high-density genetic map constructed from molecular markers. The density of the genetic map is higher, making it more favorable to QTL mapping for important agronomic traits.The population used for the construction of the genetic map is usually a segregated population for the target trait and the genetic differences between the parents should be contrast. In principle, parents with large morphological differences and distant relationship should be selected so that there is a high level of DNA polymorphism between the parents, facilitating segregation analysis and the construction of genet-ic linkage maps. However, if the parents are too different and too distantly related, chromosome pairing and recombination will be inhibited, resulting in a lower rate of recombination between linked loci; too little difference between parents will reduce DNA polymorphism between parents, affecting mapping density and the accuracy of subsequent QTL mapping. The genus of Actinidia Lindl. is highly heterozy- gous, with a large number of trait segregations being generated in the F1 generation. Due to long juvenile period of the Actinidia, it is difficult to generate mapping populations with more generations, so most of the Actinidia populations currently commonly used for mapping are F1 populations. Many traits in plants are quantitative, the basic principle of QTL mapping is to map the QTL of traits by linked mo-lecular markers of known positions on the genome. The QTL mapping is usually carried out by a compre- hensive analysis combining different methods, including QTL composite interval mapping and multiple interval mapping. Theoretically, the accuracy of mapping increases as the generations of the mapping population increase; in addition, the accuracy of QTL mapping is higher as more complex mathematical model is used for QTL mapping analysis. With the improvement of the genetic map, QTL mapping has been widely used in the field of the Actinidia. This paper reviews the application of molecular markers in kiwifruit breeding. For example, molecular markers like SCAR and SSR can be used for early sex identi-fication of the Actinidia before flowering. As the Actinidia is dioecious and heterozygous, contamination is likely to appear in the hybrid offspring due to mechanical and biological mixing during crosses, the use of InDel molecular markers with polymorphism can be effective in identifying the authenticity of hybrid offspring. In addition, an increasing number of Actinidia genetic maps have been constructed using molecular markers. This article lists 10 genetic linkage maps that have been constructed for the Actinidia. High density of genetic linkage map is a prerequisite for QTL mapping. This paper summarizes the genetic loci that have been located for quantitative traits and compares the current research advances in QTL mapping with regard to kiwifruit breeding. For example, QTL mapping has successfully been used to identify two male-specific genetic regions in diploid and tetraploid Actinidia, which are now used to predict sex at the juvenile period. A number of QTL loci associated with fruit quality traits were also lo-cated. Although quantitative traits in tetraploid Actinidia, have been studied for a long time, and the de-velopment of molecular marker technology in recent years has created the conditions for in-depth stud-ies on the inheritance patterns of quantitative traits, however, research on quantitative traits in tetraploid Actinidia, is still in the exploratory stage, the main reason is that the genetic basis of polyploids is com- plicated than diploids, and the available analysis tools for linkage map construction and QTL mapping are generally only applicable for diploids. Therefore, in the future, emphasis should be placed on the use of more efficient gene sequencing and genotyping techniques, such as gene chip technology, the develop-ment of QTL mapping tools for dissecting genetics of polyploid kiwifruit and the establishment of sys-tematic quantitative trait QTL mapping based on different temporal and spatial environments, so that static and dynamic mapping can be combined, etc. The construction and refinement of Actinidia genetic linkage maps and the rise and development of QTL mapping have provided theories and methods to im-prove the efficiency of selection and breeding of new kiwifruit varieties with high quality.