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Background The two-line method based on the photoperiod and thermo-sensitive genic male sterile (PTGMS) lines is more cost-effective, simple, and efficient than the three-line system based on cytoplasmic male-sterility. Blast and drought are the most prevalent biotic and abiotic stress factors hampering rice production. Molecular techniques demonstrate higher efficacy in the pyramiding of disease resistance genes, providing green performance under the background of water-saving and drought-resistance rice. Results This study employed molecular marker-assisted selection, conventional hybridization, and high-intensity stress screening to integrate three broad-spectrum blast resistance genes Pi9, Pi5, and Pi54 into Huhan 1S. Subsequently, a novel water-saving and drought-resistance rice (WDR) PTGMS line Huhan 74S was developed. The drought resistance of the new PTGMS line Huhan 74S was comparable to that of Huhan 1S. Pathogenicity assays involving the inoculation of 14 blast prevalent isolates in the glasshouse showed that the blast resistance frequency of Huhan 74S was 85.7%. Further evaluation under natural blast epidemic field conditions showed that Huhan 74S and its hybrids were resistant to leaf and neck blast. The critical temperature point of fertility-sterility alteration of Huhan 74S was 23 °C daily mean temperature. The complete male sterility under natural growth conditions in 2017 at Shanghai lasted for 67 days. Also, both the agronomic and grain quality traits met the requirement for two-line hybrid rice production. Conclusion These results indicate that the newly bred PTGMS line Huhan 74S can be used to breed high-yielding, good-quality, disease-resistant two-line hybrid water-saving and drought-resistance rice (WDR), hence promoting sustainable rice production in China.

Functional markers, which are designed using polymorphic sites in gene sequences and which result in phenotypic variation, have high efficiency in marker-assisted selection (MAS). xa5 is a recessive gene that confers broad-spectrum resistance to bacterial blight, and it has been widely used in rice breeding projects in all tropical regions. In this study, two functional markers [Tetra primer amplification refractory mutation system polymerase chain reaction (ARMS-PCR) and kompetitive allele specific PCR (KASP)] were developed based on the variation of two bases in the coding region of the xa5 allele. The specificity and applicability of the two functional markers were verified in a breeding segregating population and a rice micro-core germplasm resource population. We conclude that these two newly-developed functional markers can effectively determine the homozygosity and heterozygosity of the target gene under different laboratory conditions. Thus, they can be used for genotyping the xa5 gene in molecular breeding programmes, thereby improving breeding efficiency.

Background Stigma exsertion rate (SER) is a key determinant of outcrossing in hybrid rice seed production. A quantitative trait locus (QTL) for stigma exsertion rate in rice, qSER-7, has previously been detected on chromosome 7 by using a F2 population derived from two indica cytoplasmic male sterility (CMS) maintainers, Huhan 1B and II-32B. Results The chromosomal location of qSER-7 was precisely delimited by fine-scale mapping. Near-isogenic lines (NILs) were established, one of which isolated the locus in the qSER-7II-32B line, which contains an introgressed segment of II-32B in the Huhan 1B genetic background, and exhibits a significantly higher stigma exsertion rate than that of the recurrent parent. Using 3192 individuals from the BC4F2 segregation population, the QTL qSER-7 was narrowed down to a 28.4-kb region between the markers RM3859 and Indel4373 on chromosome 7. According to the rice genome annotation database, three genes were predicted within the target region. Real-time PCR analysis showed significantly higher expression levels of LOC_Os07g15370 and LOC_Os07g15390 in II-32B than in Huhan 1B. LOC_Os07g15370(OsNRAMP5) was a previously reported gene for Mn and Cd transporter. The stigma exertion rates of OsNRAMP5-overexpressing plants were significantly higher than that of wild type plants, in contrast, a T-DNA insertion mutant osnramp5 showed a lower stigma exertion rate. Conclusions In the present study, the QTL qSER-7 was isolated to a region between the markers RM3859 and Indel4373. Two candidate genes were selected based on the expression difference between the two parents, which can facilitate the further cloning of the gene underlying the quantitative trait associated with qSER-7 as well as the marker-assisted transfer of desirable genes for stigma exsertion rate improvement in rice. Electronic supplementary material The online version of this article (10.1186/s12284-019-0304-z) contains supplementary material, which is available to authorized users.

Low amylose content (AC) is a desirable trait for rice (Oryza sativa L.) cooking quality and is selected in soft rice breeding. The Wx hp allele was derived from a Yunnan rice landrace in China, Haopi, with low AC. To efficiently and rapidly utilize the low amylose content-associated gene Wx hp in rice molecular breeding programs, we developed a tetra-primer amplification refractory mutation system-polymerase chain reaction (ARMS-PCR) method, according to the single-nucleotide variation of the Wx hp . Four Wx hp -specific primers were used to perform PCR assays using genomic DNA extracted from several rice varieties. Based on the band pattern of the amplified products after electrophoresis, this method can accurately distinguish three Wx hp -related genotypes (i.e., Wx hp homozygotes, Wx hp heterozygotes, and wild-type), and the genotypes completely correspond to the appearance of mature endosperm. This method represents a novel approach that is both inexpensive and highly efficient and can be widely used for genotyping Wx hp alleles in rice germplasm collections and may aid breeding programs with marker-assisted selection (MAS).

The resource and environmental challenges faced by rice production call for resource-saving and environment-friendly rice varieties. Water-saving and drought-resistance rice (WDR) is a new type of cultivated rice combining both high yield potential and acceptable grain quality as a current lowland paddy rice, as well as water-saving and drought resistance as a traditional upland rice. The lowland and upland rice are two ecotypes adapted to contrasting soil water status, originating mainly because of their differentiated drought resistance. Upland rice, domesticated in a water–limited environment and experiencing a bidirectional selection process, has better drought resistance and especially better drought avoidance. Though the potential tradeoff between drought resistance and productivity is very common in rice, the bidirectional selection could overcome this tradeoff and accumulate recombination genotypes. It is very important to choose elite parents on the basis of studies on the great genetic diversity of rice yield and drought resistance among the rice germplasm resources and adapt the bidirectional selection strategies to especially integrate drought avoidance, drought tolerance, high water use efficiency, and productivity in WDR breeding. The breeding history and genomic studies indicated that lowland paddy rice and upland rice hybridization breeding with suitable selection in different environments is an effective approach to improving complex traits such as yield potential and drought resistance. Meanwhile, molecular technology shows higher efficiency on value-added breeding such as transferring and pyramiding pest- and disease-resistant genes, which helps WDR obtain other green characters. Twenty-two WDR varieties were registered and distributed to farmers in recent years and could be planted in both irrigated and rainfed ecosystems, thus showing promising application prospects. The major crop management technology of WDR in lowland paddy fields with water-saving cultivation and in rainfed fields by dry seeding with aerobic cultivation were also discussed in this article.

Salinity is one of the most important abiotic stress affecting the world rice production. The cultivation of salinity-tolerant cultivars is the most cost-effective and environmentally friendly approach for salinity control. In recent years, CRISPR/Cas9 systems have been widely used for target-site genome editing; however, their application for the improvement of elite rice cultivars has rarely been reported. Here, we report the improvement of the rice salinity tolerance by engineering a Cas9-OsRR22-gRNA expressing vector, targeting the OsRR22 gene in rice. Nine mutant plants were identified from 14 T0 transgenic plants. Sequencing showed that these plants had six mutation types at the target site, all of which were successfully transmitted to the next generations. Mutant plants without transferred DNA (T-DNA) were obtained via segregation in the T1 generations. Two T2 homozygous mutant lines were further examined for their salinity tolerance and agronomic traits. The results showed that, at the seedling stage, the salinity tolerance of T2 homozygous mutant lines was significantly enhanced compared to wild-type plants. Furthermore, no significantly different agronomic traits were found between T2 homozygous mutant lines and wild-type plants. Our results indicate CRISPR/Cas9 as a useful approach to enhance the salinity tolerance of rice.

The drought tolerance (DT) of plants is a complex quantitative trait. Under natural and artificial selection, drought tolerance represents the crop survival ability and production capacity under drought conditions (Luo, 2010). To understand the regulation mechanism of varied drought tolerance among rice genotypes, 95 diverse rice landraces or varieties were evaluated within a field screen facility based on the ‘line–source soil moisture gradient’, and their resistance varied from extremely resistant to sensitive. The method of Ecotype Targeting Induced Local Lesions in Genomes (Ecotilling) was used to analyze the diversity in the promoters of 24 transcription factor families. The bands separated by electrophoresis using Ecotilling were converted into molecular markers. STRUCTURE analysis revealed a value of K = 2, namely, the population with two subgroups (i.e., indica and japonica), which coincided very well with the UPGMA clusters (NTSYS-pc software) using distance-based analysis and InDel markers. Then the association analysis between the promoter diversity of these transcription factors and the DT index/level of each variety was performed. The results showed that three genes were associated with the DT index and that five genes were associated with the DT level. The sequences of these associated genes are complex and variable, especially at approximately 1000 bp upstream of the transcription initiation sites. The study illuminated that association analysis aimed at Ecotilling diversity of natural groups could facilitate the isolation of rice genes related to complex quantitative traits.