Response of Southeast Asian rice root architecture and anatomy phenotypes to drought stress.

Drought stress in Southeast Asia greatly affects rice production, and the rice root system plays a substantial role in avoiding drought stress. In this study, we examined the phenotypic and genetic correlations among root anatomical, morphological, and agronomic phenotypes over multiple field seasons. A set of >200 rice accessions from Southeast Asia (a subset of the 3000 Rice Genomes Project) was characterized with the aim to identify root morphological and anatomical phenotypes related to productivity under drought stress. Drought stress resulted in slight increases in the basal metaxylem and stele diameter of nodal roots. Although few direct correlations between root phenotypes and grain yield were identified, biomass was consistently positively correlated with crown root number and negatively correlated with stele diameter. The accessions with highest grain yield were characterized by higher crown root numbers and median metaxylem diameter and smaller stele diameter. Genome-wide association study (GWAS) revealed 162 and 210 significant SNPs associated with root phenotypes in the two seasons which resulted in identification of 59 candidate genes related to root development. The gene OsRSL3 was found in a QTL region for median metaxylem diameter. Four SNPs in OsRSL3 were found that caused amino acid changes and significantly associated with the root phenotype. Based on the haplotype analysis for median metaxylem diameter, the rice accessions studied were classified into five allele combinations in order to identify the most favorable haplotypes. The candidate genes and favorable haplotypes provide information useful for the genetic improvement of root phenotypes under drought stress.

Identification of Pathogenicity Loci in Magnaporthe oryzae Using GWAS with Neck Blast Phenotypic Data.

Magnaporthae oryzae (M. oryzae) is the most destructive disease of rice worldwide. In this study, one hundred and two isolates of M. oryzae were collected from rice (Oryzae sativa L.) from 2001 to 2017, and six rice varieties with resistance genes Pizt, Pish, Pik, Pib, and Pi2 were used in a genome-wide association study to identify pathogenicity loci in M. oryzae. Genome-wide association analysis was performed using 5338 single nucleotide polymorphism (SNPs) and phenotypic data of neck blast screening by TASSEL software together with haplotype block and SNP effect analysis. Twenty-seven significant SNPs were identified on chromosomes 1, 2, 3, 4, 5, 6, and 7. Many predicted genes (820 genes) were found in the target regions of six rice varieties. Most of these genes are described as putative uncharacterized proteins, however, some genes were reported related to virulence in M. oryzae. Moreover, this study revealed that R genes, Pik, Pish, and Pi2, were broad-spectrum resistant against neck blast disease caused by Thai blast isolate. Haplotype analysis revealed that the combination of the favorable alleles causing reduced virulence of isolates against IRBLz5-CA carrying Pi2 gene contributes 69% of the phenotypic variation in pathogenicity. The target regions and information are useful to develop marker-specific genes to classify blast fungal isolates and select appropriate resistance genes for rice cultivation and improvement.

Drought-Tolerance Gene Identification Using Genome Comparison and Co-Expression Network Analysis of Chromosome Substitution Lines in Rice.

Drought stress limits plant growth and productivity. It triggers many responses by inducing changes in plant morphology and physiology. KDML105 rice is a key rice variety in Thailand and is normally grown in the northeastern part of the country. The chromosome segment substitution lines (CSSLs) were developed by transferring putative drought tolerance loci (QTLs) on chromosome 1, 3, 4, 8, or 9 into the KDML105 rice genome. CSSL104 is a drought-tolerant line with higher net photosynthesis and leaf water potential than KDML105 rice. The analysis of CSSL104 gene regulation identified the loci associated with these traits via gene co-expression network analysis. Most of the predicted genes are involved in the photosynthesis process. These genes are also conserved in Arabidopsis thaliana. Seven genes encoding chloroplast proteins were selected for further analysis through characterization of Arabidopsis tagged mutants. The response of these mutants to drought stress was analyzed daily for seven days after treatment by scoring green tissue areas via the PlantScreen™ XYZ system. Mutation of these genes affected green areas of the plant and stability index under drought stress, suggesting their involvement in drought tolerance.

High Performance of Photosynthesis and Osmotic Adjustment Are Associated With Salt Tolerance Ability in Rice Carrying Drought Tolerance QTL: Physiological and Co-expression Network Analysis.

Understanding specific biological processes involving in salt tolerance mechanisms is important for improving traits conferring tolerance to salinity, one of the most important abiotic stresses in plants. Under drought and salinity stresses, plants share overlapping responsive mechanisms such as physiological changes and activation of signaling molecules, which induce and transmit signals through regulator genes in a regulatory network. In this study, two near isogenic lines of rice carrying chromosome segments of drought tolerance QTL on chromosome 8 from IR68586-F2-CA-31 (DH103) in the genetic background of sensitive cultivar "Khao Dawk Mali 105; KDML105" (designated as CSSL8-94 and CSSL8-95) were used to investigate physiological responses to salt stress [namely growth, Na+/K+ ratio, water status, osmotic adjustment, photosynthetic parameters, electrolyte leakage (EL), malondialdehyde (MDA), proline and sugar accumulations], compared with the standard salt tolerant (Pokkali; PK) and their recurrent parent (KDML105) rice cultivars. Physiological examination indicated that both CSSLs showed superior salt-tolerant level to KDML105. Our results suggested that salt tolerance ability of these CSSL lines may be resulted from high performance photosynthesis, better osmotic adjustment, and less oxidative stress damage under salt conditions. Moreover, to explore new candidate genes that might take part in salt tolerance mechanisms, we performed co-expression network analysis for genes identified in the CSSL rice, and found that Os08g419090, the gene involved with tetrapyrrole and porphyrin biosynthetic process (chlorophyll biosynthetic process), Os08g43230 and Os08g43440 (encoded TraB family protein and cytochrome P450, respectively) might have unprecedented roles in salt stress tolerance.

Thai Hom Mali Rice: Origin and Breeding for Subsistence Rainfed Lowland Rice System.

The world-renowned Thai Hom Mali Rice has been the most important aromatic rice originating in Thailand. The aromatic variety was collected from Chachoengsao, a central province, and after pure-line selection, it was officially named as Khao Dawk Mali 105, (KDML105). Because of its superb fragrance and cooking quality, KDML105 has been a model variety for studying genes controlling grain quality and aroma. The aromatic gene was cloned in KDML105, as an amino aldehyde dehydrogenase (AMADH) or better known as BADH2 located on chromosome 8. Later on, all other aromatic rice genes were discovered as allelic to the AMADH. As a selection of local landrace variety found in rainfed areas, the Thai Jasmine rice showed adaptive advantages over improved irrigated rice in less fertile lowland rainfed conditions. Because KDML105 was susceptible to most diseases and insect pests, marker-assisted backcross selection (MABC) was used for the genetic improvement since 2000. After nearly 17 years of MABC for integrating new traits into KDML105, a new generation of KDML105, designated HM84, was developed which maintains the cooking quality and fragrance, and has gained advantages during flash flooding, disease, and insect outbreak.

Salt-responsive mechanisms in chromosome segment substitution lines of rice (Oryza sativa L. cv. KDML105).

Two chromosome segment substitution lines of Khao Dawk Mali 105 (KDML105) rice that carry quantitative trait loci for drought tolerance located on chromosome 8 (DT-QTL8) designated CSSL8-94 and CSSL8-116 were investigated for co-expression network and physiological responses to salinity compared to their parents (KDML105; drought and salt sensitive recurrent parent, and DH103; drought tolerant QTL donor). These CSSL lines show different salt-response traits under salt stress (CSSL8-94 shows higher tolerance than CSSL8-116) and possess different segments of DT-QTL8. To identify specific biological process(es) associated with salt-stress response, co-expression network analysis was constructed from each DT-QTL segment. To evaluate differential physiological mechanisms responding to salt stress, all rice lines/cultivar were grown for 21 d in soils submerged in nutrient solutions, then subjected to 150 mM NaCl for 7 d. Physiological parameters related to co-expression network analysis (photosynthetic parameters) and salt responsive parameters (Na(+)/K(+) ratio, proline content, malondialdehyde and ascorbate peroxidase activity; EC1.11.1.1) were investigated along with the expression analysis of related genes. Physiological responses under salt stress particularly photosynthesis-related parameters of CSSL8-94 were similar to DH103, whereas those of CSSL8-116 were similar to KDML105. Moreover, expression levels of photosynthesis-related genes selected from the co-expression networks (Os08g41460, Os08g44680, Os06g01850, Os03g07300 and Os02g42570) were slightly decreased or stable in CSSL8-94 and DH103 but were dramatically down-regulated in CSSL8-116 and KDML105. These differential responses may contribute to the photosynthesis systems of CSSL8-94 being less damaged under salt stress in comparison to those of CSSL8-116. It can be concluded that the presence of the specific DT-QTL8 segment in CSSL8-94 not only confers drought tolerant traits but also enhances its salt tolerant ability.