Jonaliza L. Siangliw

Molecular Breeding for Rainfed Lowland Rice in the Mekong Region

Abstract 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 rainfed 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.

Evaluation of Agronomic Traits in Chromosome Segment Substitution Lines of KDML105 Containing Drought Tolerance QTL under Drought Stress

Drought is a major abiotic constraint to rice production in rainfed lowland and insufficiently irrigated areas. The improvement of drought tolerant varieties is one of the strategies to reduce the negative effects of drought. Quantitative trait loci (QTLs) for primary and secondary traits related to drought tolerance (DT) on chromosomes 1, 3, 4, 8 and 9 that determined from double haploid lines derived from a cross between CT9993 and IR62266 were introgressed and dissected into small pieces in the genetic background of Khao Dawk Mali 105 (KDML105) to develop chromosome segment substitution line (CSSL) population. The CSSLs were evaluated at the reproductive stage for their agronomic performance and yield components under drought stress, and results were compared with irrigated condition. The flowering of CSSL lines was 6 to 7 d earlier than KDML105. The mean values of grain yields in the CSSLs were higher than KDML105 under drought and irrigated conditions. At irrigated condition, the grain yields of introgression lines carrying DT-QTLs from chromosomes 4 and 8 were higher than that of KDML105, whereas other traits showed little difference with KDML105. Analysis indicated that grain yield has positive correlation with plant height, tiller and panicle number per plant, and total grain weight per plant under drought stress while negatively correlated with days to flowering. As mentioned above, CSSLs showing good adaptation under drought stress can be used as genetic materials to improve drought tolerance in Thai rainfed lowland rice breeding program, and as materials to dissect genes underlying drought tolerance.

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.

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.

Functional roles of root plasticity and its contribution to water uptake and dry matter production of CSSLs with the genetic background of KDML105 under soil moisture fluctuation

ABSTRACT Soil moisture fluctuation (SMF) stress due to erratic rainfall in rainfed lowland (RFL) rice ecosystems negatively affect production. Under such condition, root plasticity is one of the key traits that play important roles for plant adaptation. This study aimed to evaluate root plasticity expression and its functional roles in water uptake, dry matter production and yield under SMF using three chromosome segment substitution lines (CSSLs) with major genetic background of KDML105 and a common substituted segment in chromosome 8. The CSSLs showed greater shoot dry matter production than KDML105 under SMF, which was attributed to the maintenance of stomatal conductance resulting in higher grain yield. The root system development based on total root length of the CSSLs were significantly higher than that of KDML105 due to the promoted production of nodal and lateral roots. These results implied that the common substituted segments in chromosome 8 of the 3 CSSLs may be responsible for the expression of their root plasticity under SMF and contributed to the increase in water uptake and consequently dry matter production and yield. These CSSLs could be used as a good source of genetic material for drought resistance breeding programs targeting rainfed lowland condition with fluctuating soil moisture environments and for further genetic studies to elucidate mechanisms underlying root plasticity.