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.