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

Molecular Breeding for Rainfed Lowland Rice in the Mekong Region

In the past 20 years, the rice-breeding program in Thailand had little success in developing new cultivars to replace Kao Dawk Mali 105 (KDML105) and Kao Khor 6 (RD6) for the tainted lowland rice environments. The main reason for the poor adoption of new cultivars by farmers is the susceptibility to diseases and unacceptable grain qualities. The conventional breeding program also takes at least 15 years from initial crossing to the release of new cultivars. A new breeding strategy can be established to shorten the period for cultivar improvement by using marker-assisted selection (MAS), rapid generations advance (RGA), and early generation testing in multi-locations for grain yield and qualities. Four generation of MAS backcross breeding were conducted to transfer genes and QTL for bacterial blight resistance (BLB), submergence tolerance (SUB), brown plant hopper resistance (BPH) and blast resistance (BL) into KDML105. Selected backcross lines, introgressed with target gene/QTL, were tolerant to SUB and resistant to BLB, BPH and BL. The agronomic performance and grain quality of these lines were as good as or better than KDML105

Chlorophyll Retention and High Photosynthetic Performance Contribute to Salinity Tolerance in Rice Carrying Drought Tolerance Quantitative Trait Loci (QTLs)

Jasmine rice (Oryza sativa L.), or Khao Dawk Mali 105 (KDML105), is sensitive to drought and salt stresses. In this study, two improved drought-tolerant chromosome segment substitution lines (CSSLs) of KDML105 (CSSL8-103 and CSSL8-106), which carry drought tolerance quantitative trait loci (QTLs) on chromosome 8, were evaluated for salt tolerance and were compared with KDML105 and the QTL donor DH103, their parents and the salt-tolerant genotype Pokkali. After being subjected to salt stress for 6 days, 3-week-old seedlings of Pokkali showed the highest salt tolerance. Parameters related to photosynthesis were less inhibited in both CSSLs and the donor DH103, while these parameters were more severely damaged in the recurrent parent KDML105. Albeit a high ratio of Na+/K+, CSSLs and DH103 showed similar or higher contents of soluble sugar and activity of superoxide dismutase (SOD; EC1.15.1.1) compared with Pokkali, indicating possible mechanisms of either tissue or osmotic tolerance in these plants. The expression of a putative gene Os08g41990 (aminotransferase), which is located in DT-QTL and is involved in chlorophyll biosynthesis, significantly decreased under salt stress in KDML105 and CSSL8-103, while no obvious change in the expression of this gene was observed in Pokkali, DH103 and CSSL8-106. This gene might play a role in maintaining chlorophyll content under stress conditions. Taken together, the results of this study indicate that DT-QTL could contribute to the enhancement of photosynthetic performance in CSSL lines, leading to changes in their physiological ability to tolerate salinity stress

Root Characterization of Myanmar Upland and Lowland Rice in Relation to Agronomic and Physiological Traits under Drought Stress Condition

Lowland and upland rice are the two most important rice ecotypes and are grown under different ecosystems of contrasting soil water conditions. The study aimed to characterize root morphological, anatomical, and architectural traits and shoot physiological traits related to agronomic traits in Myanmar lowland and upland rice under drought conditions. Drought experiments were conducted in the field and in the greenhouse. The reduction in root traits under drought was observed in both lowland and upland rice except for the stele and xylem area. Stele area and xylem area were increased under drought in lowland rice while stele area in upland rice was decreased and was not changed in the xylem area. A positive relationship between agronomic traits and root traits of lowland rice was observed including the total number of nodal roots, root number per tiller, and a negative relationship in lateral root density more than anatomical traits. While upland rice illustrated the relationship between root anatomical traits and agronomic traits. In addition, a negative contribution to biomass by photosynthesis rate, stomatal conductance, and transpiration rate was observed in lowland and upland rice. These findings can help improve drought tolerance in rice by selecting the optimal root trait for each rice ecosystem

Effects of drought tolerant quantitative trait loci on flowering traits, panicle exsertion rate, spikelet sterility and grain yield of rice under rainfed lowland conditions

Drought hinders rice production and yield stability in rainfed lowland ecosystems. Quantitative trait loci (QTL) for root traits on chromosomes 1, 2, 7 and 9 in backcross introgression lines (BIL) of elite rice variety IR64, derived from Azucena/IR64, were designated as Targets 1, 2, 7 and 9 in the present study. Severe stress developed during the period of optimum flowering as indicated by 98-100% yield reduction. Significant phenotypic variations in BIL were observed on days to flowering (DF), delay in flowering (DeF), panicle exsertion rate (PEX), percent spikelet sterility (PSS) and grain yield (GY). Variations among target QTL were also found in the traits studied, particularly under drought stress, indicating that BIL containing Targets 1 and 2 had early DF, higher PEX, lower PSS and higher GY under stress than those with Targets 7 and 9. Targets 7 and 9 lacked QTL for root thickness, indicating that it plays a role in drought tolerance under rainfed lowland conditions. Early flowering BIL had an advantage over later flowering ones because water can be extracted at the early drought stage, which can support the PEX and result in low PSS. In a very severe drought at the flowering stage, PSS directly affected GY. Further study of root morphology and early flowering under stress are necessary to improve rice yields under rainfed lowland conditions

Root Characterization of Myanmar Upland and Lowland Rice in Relation to Agronomic and Physiological Traits under Drought Stress Condition

Lowland and upland rice are the two most important rice ecotypes and are grown under different ecosystems of contrasting soil water conditions. The study aimed to characterize root morphological, anatomical, and architectural traits and shoot physiological traits related to agronomic traits in Myanmar lowland and upland rice under drought conditions. Drought experiments were conducted in the field and in the greenhouse. The reduction in root traits under drought was observed in both lowland and upland rice except for the stele and xylem area. Stele area and xylem area were increased under drought in lowland rice while stele area in upland rice was decreased and was not changed in the xylem area. A positive relationship between agronomic traits and root traits of lowland rice was observed including the total number of nodal roots, root number per tiller, and a negative relationship in lateral root density more than anatomical traits. While upland rice illustrated the relationship between root anatomical traits and agronomic traits. In addition, a negative contribution to biomass by photosynthesis rate, stomatal conductance, and transpiration rate was observed in lowland and upland rice. These findings can help improve drought tolerance in rice by selecting the optimal root trait for each rice ecosystem

Physiological Responses under Drought Stress of Improved Drought-Tolerant Rice Lines and their Parents

Many of the economically important rice cultivars including ‘Khao Dawk Mali 105’ (KDML105) or jasmine rice, one of the world’s famous rice exported from Thailand suffers from drought due to erratic rainfalls and limited irrigation. To improve drought tolerance and reserve genetic background of KDML105, chromosome segment substitution lines (CSSL) containing drought tolerant quantitative trait loci (DT-QTL) has been previously developed by backcrossing between KDML105 and drought tolerant donor, IR58586-F2-CA-143 (DH212). To understand the physiological responses related to drought tolerance in CSSL lines compared to parents, two CSSLs namely CSSL1-16 and CSSL1-18, respectively were used in this study. Twenty-one-d-old hydroponically grown plants were subjected to 20% PEG for 0, 7, 14 d and then recovered from stress for 3 d. The results indicated that CSSL lines especially, CSSL1-16 showed better performance under drought stress compared to their recurrent parent. Drought tolerance superior CSSL1-16 line was indicated by high water status (high relative water content and leaf water potential), good osmotic adjustment, high proline and greater membrane stability. Moreover, this line was able to resume growth after stress recovery whereas other lines/cultivar could not recover. Similarly, drought tolerant donor showed high water status suggesting that well-maintained plant water status was associated with drought tolerant trait. It could be concluded that the highest drought tolerant line was CSSL1-16 followed by DH212, CSSL1-18 and KDML105. It would be interesting to go further into introgressed section in CSSL1-16 to identify potential candidate genes in DT-QTL for breeding drought tolerant rice in the future

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

Abstract 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

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

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