Introduction
Rice, which is a very important and common crop, is grown in many countries and regions of the world, especially in China. There is wide genetic variation amongall plant species, especially for rices. The genus Oryzais is more wildely grown among all rice species , and also shows higher genetic diversity, so it is often regarded as a valuable resource for rice improvement (Brar, 2003; Sun et al . 2001). Using wild rice in breeding programs can facilitate adaptation of rice to climate change and meet the demand for food security in the face of rapid world population growth (Henry, 2016; Moner et al . 2018). Some previous studies have revealed that members of the genusOryzais can provide a rich repository of genes and alleles for potential utilization in rice improvement with the help of genomics-assisted breeding (Lam et al . 2018). For example, in recent years, several quantitative trait locus (QTL) studies have revealed that O. rufpogon has genetic potential for improving yield-related traits (Shishido et al . 2019). These results are in accordance with some previous studies which showed that O. rufpogon from the low-yielding had more beneficial effects thanO. sativa in different elite cultivars (Fu et al. 2010, Xie et al. 2008). Some alleles which contributed to early spikelet opening times of wild rice were detected by Thanh et al., (Thanh et al. 2010). Their study results showed that this trait is useful for changing cultivar flowering times to avoid pollen sterility at high temperatures. Moreover, three novel alleles which enhanced the phosphorus uptake efficiency of O. rufpogon were also reported by Neelam et al., (Neelamet al. 2017). These above-mentioned alleles will promote a better understanding ecological diversity of rice, and provide useful gene markers for further studies of the genetic diversity and genetic structure of rice.
Generally, genetic variation is a very common phenomenon. There are many species of organisms which exhibit greater genetic variations including animals and plants. Rice, as a more common of plant type in the natural environment, must exhibit genetic variations. Presently, for identification and differentiation of rice species, we often employ traditional methods that are based mainly on morphological features, such as the color of rice leaves, and their shapes . However, applying these criteria to identify and distinguish organisms which have similar morphology or are at different stages of development is sometimes difficult for non-specialists, especially for rices with very similar morphologies. The Oryzais are the largest genus in the rice family, and their members have similar morphologies, so we sometimes don’t identify and distinguish them by traditional methods. In addition, we also can’t clearly know the taxonomic status and evolutionary relationship of new rice species and wild rice using morphological methods. Molecular techniques not only overcome the limitations of traditional methods, but also provide alternative approaches for accurate identification and differentiation of many species of crops with very similar morphologies. Many gene markers are widely used as a powerful tool to study the genetic diversity, population structures and genetics of crop species (Gao et al, 2004; Song et al. 2003; Kaewcheenchai et al., 2018). In fact, some previous studies have used some genes from the chloroplast (cp) genome as powerful gene markers to monitor transition in population structures in nature (Orn et al., 2015; Wang et al., 2012). For example, Shishido et al., used two chloroplast DNA markers (e.g., ORF100 and ORF29-trn C) to study genetic diversity and genetic structure of wild rice populations in Myanmar (Shishido et al. 2019). China is a large agricultural country and large rice breeding country where rice is widely grown, but there is a paucity of information regarding chloroplast (cp) genome sequence variations, genetic diversity and genetic structures of rice.
The chloroplast (cp) genome contains three functional categories which include protein-coding genes, introns and intergenic spacers; the latter two do not encode proteins and are often referred to as non-coding regions but the genes of non-coding regions show that their nucleotide substitution rates are 2.3 times higher than those of protein-coding genes, so some gene sequences from the non-coding regions have been used to study genetic diversity, genetic structures and population structures of organisms. For example, the use of non-coding chloroplast DNA sequences to generate plant phylogenies began in the early 1990s (Taberlet et al. 1991; Clegg et al. 1994; Gielly and Taberlet. 1994). Shaw et al. used 21 non-coding region genes of chloroplast (cp) genomes to study the interspecific phylogenetic and intraspecific phylogeography of Nicotiana in 2007 (Shaw et al. 2007). Moreover, some research clearly indicates that non-coding cpDNA sequences have been used in molecular systematic research of plants for more than 15 years (Shaw et al. 2007). This evidence has suggested that non-coding gene sequences can provide powerful gene markers to study genetic diversity, genetic structures and population structures of organisms. According to the chloroplast map drawn by Shaw, the aptH gene is in a non-coding region and the aptH gene belongs to a non-coding gene. So, we used the atpH gene sequence as a gene marker to study the genetic diversity and genetic structure of B810S in this study.
The objectives of the present study were (a) to clarify the genetic diversity of B810S, and (b) reveal the genetic structure of B810S in China by using cytoplasmic markers. In addition, the results of the current study should provide a foundation for studying the genetic diversity and genetic structure of rice with different geographical origins in China and other regions of the world. Moreover, our study results also provide insight into mutational rice resources that could be useful for biological conservation as well as exploitation in rice breeding programs.