Genomic and transcriptomic analysis reveal molecular basis of salinity tolerance in a novel strong salt-tolerant rice landrace Changmaogu.

BACKGROUND: Salt stress is an important factor that limits rice yield. We identified a novel, strongly salt tolerant rice landrace called Changmaogu (CMG) collected from a coastal beach of Zhanjiang, Guangdong Province, China. The salt tolerance of CMG was much better than that of the international recognized salt tolerant rice cultivar Pokkali in the germination and seedling stages. RESULTS: To understand the molecular basis of salt tolerance in CMG, we performed BSA-seq for two extreme bulks derived from the cross between CMG and a cultivar sensitive to salt, Zhefu802. Transcriptomic sequencing was conducted for CMG at the germination and young seedling stages. Six candidate regions for salt tolerance were mapped on Chromosome 1 by BSA-seq using the extreme populations. Based on the polymorphisms identified between both parents, we detected 32 genes containing nonsynonymous coding single nucleotide polymorphisms (SNPs) and frameshift mutations in the open reading frame (ORF) regions. With transcriptomic sequencing, we detected a large number of differentially expressed genes (DEGs) at the germination and seedling stages under salt stress. KEGG analysis indicated two of 69 DEGs shared at the germination and seedling stages were significantly enriched in the pathway of carotenoid biosynthesis. Of the 169 overlapping DEGs among three sample points at the seedling stage, 13 and six DEGs were clustered into the pathways of ABA signal transduction and carotenoid biosynthesis, respectively. Of the 32 genes carrying sequence variation, only OsPP2C8 (Os01g0656200) was differentially expressed in the young seedling stage under salt stress and also showed sequence polymorphism in the ORFs between CMG and Zhefu802. CONCLUSION: OsPP2C8 was identified as the target candidate gene for salinity tolerance in the seedling stage. This provides an important genetic resource for the breeding of novel salt tolerant rice cultivars.

Genome-wide DNA polymorphism in the indica rice varieties RGD-7S and Taifeng B as revealed by whole genome re-sequencing.

Next-generation sequencing technologies provide opportunities to further understand genetic variation, even within closely related cultivars. We performed whole genome resequencing of two elite indica rice varieties, RGD-7S and Taifeng B, whose F1 progeny showed hybrid weakness and hybrid vigor when grown in the early- and late-cropping seasons, respectively. Approximately 150 million 100-bp pair-end reads were generated, which covered ∼86% of the rice (Oryza sativa L. japonica 'Nipponbare') reference genome. A total of 2,758,740 polymorphic sites including 2,408,845 SNPs and 349,895 InDels were detected in RGD-7S and Taifeng B, respectively. Applying stringent parameters, we identified 961,791 SNPs and 46,640 InDels between RGD-7S and Taifeng B (RGD-7S/Taifeng B). The density of DNA polymorphisms was 256.8 SNPs and 12.5 InDels per 100 kb for RGD-7S/Taifeng B. Copy number variations (CNVs) were also investigated. In RGD-7S, 1989 of 2727 CNVs were overlapped in 218 genes, and 1231 of 2010 CNVs were annotated in 175 genes in Taifeng B. In addition, we verified a subset of InDels in the interval of hybrid weakness genes, Hw3 and Hw4, and obtained some polymorphic InDel markers, which will provide a sound foundation for cloning hybrid weakness genes. Analysis of genomic variations will also contribute to understanding the genetic basis of hybrid weakness and heterosis.

Expression of MyHC genes, composition of muscle fiber type and their association with intramuscular fat, tenderness in skeletal muscle of Simmental hybrids.

In adult bovine skeletal muscle, it expressed four isoforms of Myosin heavy chain (MyHC) gene, MyHC-I, MyHC-IIa, MyHC-IIb, and MyHC-IIx that are translated into different structural protein myofibrils, and then further form different types of muscle fiber. In the studies, our objective is to reveal the expression patterns of MyHC genes in longissimus dorsi (Ld), semitendinosus (Se) and soleus (Sol) of Simmental hybrids cattle, and their association with intramuscular fat (IMF) content and meat shearing force (MSF). The muscle tissue of Ld, Se and Sol were collected from 6, 12 and 36-month old Simmental hybrids respectively, then the expression levels of MyHCs were examined by real-time PCR, at the same time, IMF, MSF and muscle type were measured with chemical assessment, shearing force measurer and immunostaining respectively. Our results showed that t Ld, Se, and Sol expressed MyHC-I, MyHC-IIa and MyHC-IIx isoforms but not MyHC-IIb, furthermore MyHC-I, MyHC-IIa and MyHC-IIx had different expression patterns in different skeletal muscle. The expression of MyHC-I in Se and Sol, MyHC-IIa in Ld, Se, and Sol, and MyHC-IIx in Sol was decreased with increasing age. The highest expression of MyHC-I in Ld, and MyHC-IIx in Ld and Se was observed in 12-month-old animals. The percentage of type-IIa fiber approximately occupied 70-80 % among various muscle fiber of Ld, Se and Sol. The percentage of different type fiber was not related to IMF content and MSF, but the expression levels of MyHC-I and MyHC-IIa were negatively related to IMF content (r = -0.724, and -0.681, respectively) and MSF (r = -0.672, and -0.641, respectively). The expression level of MyHC-IIx was also negatively related to MSF (r = -0.655). In conclusion, MyHC gene might be considered as a negative factor in genetic selection of IMF content and MSF.

Genetic and cytological analysis of a novel type of low temperature-dependent intrasubspecific hybrid weakness in rice.

Hybrid weakness (HW) is an important postzygotic isolation which occurs in both intra- and inter-specific crosses. In this study, we described a novel low temperature-dependent intrasubspecific hybrid weakness in the F1 plants derived from the cross between two indica rice varieties Taifeng A and V1134. HW plants showed growth retardation, reduced panicle number and pale green leaves with chlorotic spots. Cytological assay showed that there were reduced cell numbers, larger intercellular spaces, thicker cell walls, and abnormal development of chloroplast and mitochondria in the mature leaves from HW F1 plants in comparison with that from both of the parental lines. Genetic analysis revealed that HW was controlled by two complementary dominant genes Hw3 from V1134 and Hw4 from Taifeng A. Hw3 was mapped in a 136 kb interval between the markers Indel1118 and Indel1117 on chromosome 11, and Hw4 was mapped in the region of about 15 cM between RM182 and RM505 on chromosome 7, respectively. RT-PCR analysis revealed that only LOC_Os11g44310, encoding a putative calmodulin-binding protein (OsCaMBP), differentially expressed among Taifeng A, V1134 and their HW F1. No recombinant was detected using the markers designed based on the sequence of LOC_Os11g44310 in the BC1F2 (Taifeng A//Taifeng A/V1134) population. Hence, LOC_Os11g44310 was probably the candidate gene of Hw3. Gene amplification suggested that LOC_Os11g44310 was present in V1134 and absent in Taifeng A. BLAST search revealed that LOC_Os11g44310 had one copy in the japonica genomic sequence of Nipponbare, and no homologous sequence in the indica reference sequence of 9311. Our results indicate that Hw3 is a novel gene for inducing hybrid weakness in rice.

[Genetic analysis and mapping of a rice white midrib mutant Oswm2].

A rice (Oryza sativa L.) plant with white midrib (Oswm2) was selected from the T-DNA inserted mutant pool of rice. The basal midrib of the leaves in the mutant, except for the flag leaves, is white. The blade close to the white midrib is etiolated, and alterations of the agronomic traits, such as plant height, panicle length occur in the mutant. Genetic analysis indicated that this mutant trait was controlled by a recessive nuclear gene. To map the OsWM2 gene, an F2 population was constructed by crossing mutant Oswm2 with 02428. The OsWM2 locus was preliminarily located between the SSR molecular markers RM21478 and RM418 on chromosome 7 with the distances of 8.7 and 15.9 cM, respectively.