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.     

Ideotype breeding for submergence tolerance and cooking quality by marker-assisted selection in rice

Submergence tolerance and jasmine-like cooking quality are desirable for rice varieties grown in rainfed and irrigated lowland ecosystems in the Mekong region of Southeast Asia. Hybridization between varieties IR57514 and Kao Dawk Mali 105 (KDML105) was initiated with the goal of producing an ideotype that combines submergence tolerance and jasmine-like cooking quality. Through the single seed descent (SSD) method, a large population of recombinant inbred lines (RILs) was developed, and we demonstrated the potential of using marker-assisted selection (MAS) in the identification of the ideotype from the offspring. Four markers, R10783Indel, Waxy, Aromarker and GT11, were used to select the favored alleles of the Sub1, Wx, badh2 and SSIIa loci, respectively. The ideotype was classified into two groups: ideotype1 (ID1), carrying the Sub1^IR, badh2^KD, Wx^KD and SSIIa^KD alleles and consisting of 66 RILs and ideotype2 (ID2), carrying the Sub1^IR, badh2^KD, Wx^KD and SSIIa^IR alleles and consisting of 31 RILs. Submergence tolerance, cooking quality, grain quality and agronomic characteristics of the IDs were evaluated and compared with those of the parents. All of the ID1 lines exhibited submergence tolerance and jasmine-like cooking quality and displayed a low amylose content, a fragrance and a high alkali spreading value, whereas the ID2s showed the same characteristics as ID1, except for a low alkali spreading value, which was inherited from IR57514. A wide range of agronomic characteristics was observed in both of the ID groups, and some of the IDs were superior in the yield component, as compared to their parents. This study provides further support that the precision of markers used in MAS can enhance the development of ideotypes in rice.     

Yield, grain quality and water use efficiency of rice under non-flooded mulching cultivation

Plastic film or straw mulching cultivation under non-flooded condition has been considered as a new water-saving technique in rice production. This study aimed to investigate the yield performance in terms of quality and quantity and water use efficiency (WUE) under such practices. A field experiment across 3 years was conducted with two high-yielding rice cultivars, Zhendao 88 (a japonica cultivar) and Shanyou 63 (an indica hybrid cultivar) and four cultivation treatments imposed from transplanting to maturity: traditional flooding as control (TF), non-flooded plastic film mulching (PM), non-flooded wheat straw mulching (SM), and non-flooded no mulching (NM). Compared with those under the TF, root oxidation activity, photosynthetic rate, and activities of key enzymes in sucrose-to-starch conversion in grains during the grain filling period were significantly increased under the SM, whereas they were significantly reduced under the PM and NM treatments. Grain yield showed some reduction under all the non-flooded cultivations but differed largely among the treatments. The reduction in yield was 7.3–17.5% under the PM, 2.8–6.3% under the SM, and 39–49% under the NM. The difference in grain yield was not significant between TF and SM treatments. WUE for irrigation was increased by 314–367% under the PM, 307–321% under the SM, and 98–138% under the NM. Under the same treatment especially under non-flooded conditions, the indica hybrid cultivar showed a higher grain yield and higher WUE than the japonica cultivar. The SM significantly improved milling, appearance, and cooking qualities, whereas the PM or the NM decreased these qualities. We conclude that both PM and SM could significantly increase WUE, while the SM could also maintain a high grain yield and improve quality of rice. The SM would be a better practice than the PM in areas where water is scarce while temperature is favorable to rice growth, such as in Southeast China.     

QTL analysis of panicle morphology response to irrigation regime in aerobic rice culture

In water-efficient rice production, grain yield is often constrained by panicle size. The objective of this study was to genetically dissect the response of panicle morphology to irrigation regimes in aerobic rice culture. We grew ‘Akihikari’ (a lowland japonica cultivar) × ‘IRAT109’ (an upland japonica cultivar) backcross inbred lines in aerobic soils with full or limited irrigation for 2 years, and examined 4 panicle traits—number of florets per panicle (FPP), number of primary branches per panicle (BPP), number of florets per primary branch (FPB), and frequency of pre-flowering floret abortion (%FA)—and grain yield. QTLs for BPP were detected in both the irrigation regimes but QTLs for FPB and %FA were detected mostly only in either of the irrigation regimes. The QTL for FPP on chromosome 2 (RM3421–RM213) coincided with that for yield under full irrigation, showing that this QTL is related to sink capacity and yield potential in aerobic rice culture. On the other hand, the QTL for FPB on chromosome 1 (RM3148–RM243) coincided with that for yield under limited irrigation, when water deficit was moderate. The QTL for root axis length at vegetative stage, previously identified in the same mapping population, was located near this region. This study unravelled the complicated genetic control on panicle morphology in aerobic rice culture, and suggested the positive roles of the dehydration avoidance mechanism by vigorous root growth on panicle size and yield under dry soil conditions.     

Grain quality of rices grown in irrigated and upland cultures

Upland culture of nine varieties at Ivory Coast resulted in decreases in grain weight, brown and milled rice translucency, Chroma meter L^* of rough rice, Chroma meter L^* and b^* of milled rice, milled rice protein, and Amylograph peak viscosity, and in increases in total phenolics of hull and brown rice, and Chroma meter a^* of rough, brown, and milled rice of 5 to 8 of the varieties as compared with irrigated culture. Upland culture had no consistent effect on grain resistance to Angoumois grain moth (Sitotraga cerealella).     

Effects of Soil Clay Content on Water Balance and Productivity in Rainfed Lowland Rice Ecosystem in Northeast Thailand

Abstract

Water availability is one of the determinants of productivity of rainfed lowland rice (Oryza sativa L.). Quantifying water losses from a paddy field, such as deep percolation and lateral seepage, assists estimation of water availability to the rice crop and development of appropriate water management in the lowlands. The main objective of this study was to evaluate paddy water availability and productivity across various soils in Northeast Thailand. The daily rate of downward water flow from standing water in the field (D) varied between 0 and 3 mm day^-1 from clayey to sandy soils when the standing water was connected to groundwater table. However, when the standing water was separated from groundwater table, D increased up to 5 mm day^-1 on soils with very low clay content in the topsoil. Daily net lateral water flow from the field (L) averaged over the season varied between 5 and 24 mm day^-1 for the outflow and between 3 and 16 mm day^-1 for the inflow. Both the inflow and outflow tended to be associated negatively with the soil clay content. The seasonal water loss through D plus L during the growing season in the lowlands was also negatively related to the soil clay content. The yield of a major rainfed lowland rice cultivar in Northeast Thailand (KDML105) varied from 2 to 4 t ha^-1 across the region, and the water productivity (the ratio of grain yield to cumulative rainfall from transplanting/seedling establishment to maturity) ranged from 3 to 9 kg ha^-1 mm^-1. High clay soils could provide good standing water until late in the growing season, so the high production efficiency was measured on such soils.     

Yield formation of CO2-enriched hybrid rice cultivar Shanyou 63 under fully open-air field conditions

Hybrid indica rice (Oryza sativa L.) cultivars play an important role in rice production system due to its heterosis, resistance to environmental stress, large panicle and high yield potential. However, no attention has been given to its yield responses to rising atmospheric [CO₂] in conjunction with nitrogen (N) availability. Therefore we conducted a free air CO₂ enrichment (FACE) experiment at Yangzhou, Jiangsu, China (119°42′0′′E, 32°35′5′′N), in 2004–2006. A three-line hybrid indica rice cv. Shanyou 63 was grown at ambient and elevated (ca. 570 μmol mol⁻¹) [CO₂] under two levels of supplemental N (12.5 g Nm⁻² and 25 g Nm⁻²). Elevated [CO₂] had no effect on phenology, but substantially enhanced grain yield (+34%). The magnitude of yield response to [CO₂] was independent of N fertilization, but varied among different years. On average, elevated [CO₂] increased the panicle number per square meter by 10%, due to an increase in maximum tiller number under enrich [CO₂], while productive tiller ratio remained unaffected. Spikelet number per panicle also showed an average increase of 10% due to elevated [CO₂], which was supported by increased plant height and stem dry weight per tiller. Meanwhile, elevated [CO₂] caused a significant enhancement in both filled spikelet percentage (+5%) and individual grain weight (+4%). Compared with the two prior FACE studies on rice, hybrid indica rice cultivar appears to profit much more from elevated [CO₂] than japonica rice cultivar (ca. +13%), not only due to its stronger sink generation, but also enhanced capacity to utilize the carbon sources in a high [CO₂] environment. The above data has significant implication with respect to N strategies and cultivar selection under projected future [CO₂] levels.     

Mixing groundnut residues and rice straw to improve rice yield and N use efficiency

Groundnut as a pre-rice crop is usually harvested 1–2 months before rice transplanting. During this lag phase much of N in groundnut residues could be lost due to rapid N mineralization. Mixing of abundantly available rice straw with groundnut residues may be a means for reducing N and improve subsequent crop yields. The objectives of this experiment were to investigate the effect of mixing groundnut residues and rice straw in different proportions on (a) growth and yield of succeeding rice, (b) groundnut residue N use efficiency and (c) N lost (¹⁵N balance) from the plant–soil system and fate of residue N in soil fractions. The experiment consisted of six treatments: (i) control (no residues), (ii) NPK (at recommended rate, 38 kg N ha⁻¹), (iii) groundnut residues 5 Mg ha⁻¹ (120 kg N ha⁻¹), (iv) rice straw 5 Mg ha⁻¹ (25 kg N ha⁻¹), (v) 1:0.5 mixed (groundnut residues 5 Mg: rice straw 2.5 Mg ha⁻¹), and (vi) 1:1 mixed (groundnut residues 5 Mg: rice straw 5 Mg ha⁻¹). After rice transplanting, samples of the lowland rice cultivar KDML 105 were periodically collected to determine growth and nutrient uptake. At final harvest, dry weight, nutrient contents and ¹⁵N recovery of labeled groundnut residues were evaluated.     

Wx基因对灌浆期小麦不同叶位叶片光合特性的影响

为了解Wx基因对小麦光合作用的影响,对8个小麦Wx近等基因系的不同叶位叶片光合参数进行了测定和分析。结果表明,小麦叶片净光合速率、气孔导度、胞间CO2浓度和蒸腾速率在叶位和基因型间均有极显著差异,缺失单个Wx基因使叶片光合参数下降,且降幅表现为Wx-D1Wx-A1Wx-B1;胞间CO2浓度不影响光合作用,不同叶位叶片光合参数明显呈旗叶倒二叶倒三叶,但WxABD(糯小麦)光合参数在叶位间没有显著差异;Wild type和WxABD总体光合能力和产量相对较高。以上结果说明,Wx基因的缺失会引起叶片光合能力下降,不利于小麦产量形成。     

Effects of Variations in Starch Synthase on Starch Properties and Eating Quality of Rice

Abstract

We evaluated the effects of functional variation in three starch synthases in rice (Oryza sativa L.)?granule-bound starch synthase I (GBSSI, wx), starch synthase I (SSI, SSI), and starch synthase IIa (SSIIa, alk)?between indica cultivar Kasalath and japonica cultivar Nipponbare on starch properties and eating quality. We used three near-isogenic lines?NIL(Wx^a), NIL(SSI ^k), and NIL(Alk)?containing chromosomal segments of Kasalath on a Nipponbare genetic background. The Wx^a allele explained most of the difference in amylose content between the two cultivars, and decreased the peak viscosity and breakdown to less than half of those of Nipponbare. These changes reduced the quality of cooked rice both just after cooking and after storage at 5ºC. The variation in SSIIa also affected the eating quality after storage of cooked rice at 5ºC : NIL(Alk) became harder and less sticky than Nipponbare, although the rices were comparable just after cooking. Differential scanning calorimetry revealed faster retrogradation of the once-gelatinized starch in NIL(Alk). The variation in SSI alleles hardly affected these properties.     

Yield potential and water use efficiency of aerobic rice (Oryza sativa L.) in Japan

Intensive rice farming in aerobic soil, referred to herein as aerobic rice, can greatly reduce the water input compared to that of flooded rice cultivation. The objective of this study was to compare the potential productivity of aerobic rice and flooded rice using high-yielding varieties at two locations in Japan in two successive years. In aerobic fields, the total amount of water supplied (irrigation plus rainfall) was 800–1300 mm. The soil water potential at 20-cm depth averaged between −15 and −30 kPa each growing season, but frequently reached −60 kPa. The average yield under aerobic conditions was similar to or even higher than that achieved with flooded conditions (7.9 t ha⁻¹ in 2007 and 9.4 t ha⁻¹ in 2008 for aerobic versus 8.2 t ha⁻¹ for flooded). The average water productivity under aerobic conditions was 0.8–1.0 kg grain m⁻³ water, slightly higher than common values in the literature. The super-high-yielding cultivar Takanari achieved yields greater than 10 t ha⁻¹ with no yield penalty under aerobic conditions in 3 out of 4 experiments. The favorable agronomic characteristic of Takanari was its ample sink capacity (grain number × grain weight). In conclusion, high-productivity rice cultivation in aerobic soil is a promising technology for water conservation. With continued breeding, future aerobic rice varieties will possess large numbers of spikelets and sufficient adaptation to aerobic conditions such that they will consistently achieve yields comparable to the potential yield of flooded rice.     

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.     

Fusarium Species Synthesize Alkaline Proteinases in Infested Barley

Barley (Hordeum vulgare L.) that is infested with Fusarium head blight (FHB, ‘scab’) is unsuitable for malting and brewing because it may contain mycotoxins and has unacceptable malting quality. Fungal proteinases are apparently often involved in plant-microbe interactions, where they degrade storage proteins, but very little is known about the enzymes that the fungi produce in the infected grain. We have shown previously that one plant pathogenic fungus, Fusarium culmorum, produced subtilisin- and trypsin-like enzymes when grown in a cereal protein medium. To establish whether these proteinases were also synthesized in FHB-infested barley in vivo, field-grown barley was infested as the heads emerged. Extracts were prepared from the grain as it developed and matured and their proteolytic activities were measured with N-succinyl-Ala-Ala-Pro-Phe p -nitroanilide and N-benzoyl-Val-Gly-Arg p -nitroanilide. The heavily infested barleys contained both subtilisin- and trypsin-like activities. These enzymes reacted with antibodies prepared against each of the two F. culmorum proteinases, indicating that those produced in the laboratory cultures and in the field-infested barley were the same. The presence of these proteinases correlated with the degradation of specific buffer-soluble proteins in the infested grains. These enzymes readily hydrolyzed barley grain storage proteins (C- and D-hordeins) in vitro. The presence of these Fusarium proteinases in the barley indicates that they probably play an important role in the infestation, but exactly how and when they function is not clear.     

40份骨干玉米自交系对镰孢穗腐病的抗性评价

2018~2019年针对黑龙江省穗腐病自然发病率较低的40份骨干玉米自交系，通过田间人工接种手段，对其镰孢穗腐病抗性进行评价。结果表明，在分别接种禾谷镰孢菌和拟轮枝镰孢菌后，各自交系的抗性潜力存在差异，筛选出自交系83J03、HB1037、绥系617、SX718、PHT77抗穗腐病能力较强，其中，骨干自交系83J03、绥系617于不同年际间表现出稳定的高抗性，受自然环境变化的影响较小，可以作为抗原用于抗穗腐病改良选育工作中。自交系HB1124、N5针对穗腐病综合抗性较低，穗腐病高发地区需谨慎使用，为镰孢穗腐病抗性育种及种质改良提供材料基础和试验依据。     

Response of lowland rice to agronomic management under different hydrological regimes in an inland valley of Ivory Coast

A large proportion of the rice in West Africa is produced in rainfed lowland ecosystems, mainly in inland valleys. The hydrological conditions (duration and intensity of flooding) vary with the toposequence position between the fringe and the centre of the valley. Production methods tend to evolve from the currently predominant unbunded plots without external input use, to input-intensive production in bunded plots. Agronomic management interventions co-evolve and may include varietal choice, herbicide use, and mineral N fertilizer application. The response of rice and the associated weeds to such interventions is likely to vary with the prevailing hydrological regime. A 2-year field experiment was conducted in northern Ivory Coast to determine the impact of water regime (plot position in the valley, presence of bunds) and input use (mineral N fertilizer and herbicide) on the productivity (yield and N use efficiency) of traditional and modern rainfed lowland rice cultivars and the biomass and composition of the associated weeds. Installing field bunds reduced seasonal variations in ponded water depth and resulted in a mean increase in rice grain yield of 30–40% (p < 0.005). This increase was associated with a 25% lower cumulative weed biomass and a several-fold increase in the agronomic use efficiency of applied mineral N in bunded than unbunded plots. Under low input management, traditional varieties tended to out-yield modern varieties in unbunded plots. Improved crop management such as herbicide and fertilizer application, and the construction of field bunds was more effective to increase the yield and N use efficiency in the flooded valley centre than in the drought-prone valley fringes. There is a need for site-specific targeting of modern cultivars, land development and improved production methods in the inland valleys of the West African savanna zone.     

Marker assisted backcross breeding to improve cooking quality traits in Myanmar rice cultivar Manawthukha

Several components contribute to rice grain quality, and among these, fragrance and taste qualities are the most important to consumers. Manawthukha, an elite non-fragrant cultivar with high amylose content (AC), intermediate gel consistency (GC) and gelatinisation temperature (GT), occupies the largest number of acres in Myanmar. To improve fragrance and intermediate AC in Manawthukha, Basmati370 was used as a donor parent to introgress the Basmati alleles of genes conferring fragrance and intermediate AC into Manawthukha by Marker Assisted Backcrossing (MAB). Four backcrosses and one selfing were conducted to transfer positive alleles of badh2 and Wx from Basmati into Manawthukha. Twelve BC₄F₂ selected lines that carried the homozygous Basmati alleles were planted in multi-location trials (four in Myanmar and one in Thailand) and examined for their agronomic performance and cooking quality. The seeds of the improved lines and their parents, harvested from Kamphaeng Saen, Kuaukse, Kyauktada and Latpatan, were investigated for fragrance and AC. All improved lines had fragrance and intermediate AC similar to the donor parent Basmati, whereas their agronomic performances were the same as the original Manawthukha. All improved lines had medium plant heights, high tiller numbers, dense panicles, non-lodging phenotypes and high yielding potentials. Simultaneous improvement of fragrance and intermediate AC indicated that badh2 and Wx genes had major effects on the fragrance and AC, respectively. We show here the success of improving fragrance and intermediate AC by MAB and the high efficiency of selection in early generations. In the present study, MAB accelerated the development of superior qualities in the genetic background of Manawthukha. The improved Manawthukha should be immediately useful for Myanmar farmers and will help farmers to increase their incomes.     

Studies on Ipomea carnea and Cannabis sativa as an alternative pulp blend for softwood: An optimization of kraft delignification process

Ipomea carnea Jacq, a common weed known as ‘Beshram’ was introduced in India, as an ornamental plant. Surprisingly, except fiber length, other morphological characteristics like, cell wall thickness, lumen diameter, flexibility coefficient and wall fraction of I. carnea resemble with softwoods like, Pinus kesiya, and Picca abies. Cannabis sativa L., a common weed known as soft hemp consists of both bast fiber as well as core fiber. The unique morphological characteristics of I. carnea like, cell wall thickness and flexibility coefficient, which resembles with softwoods along with long fibers of C. sativa, in which I. carnea deficits in a proper blend ratio, can be used in a better way for the development of high quality value added paper. The optimum kraft cooking conditions for I. carnea and C. sativa were: active alkali 16%, sulfidity 20%, temperature 165 °C, time (at temperature) 120 min and wood to liquor ratio of 1:4 for I. carnea and 1:3.5 for C. sativa. The screened pulp yield of I. carnea and C. sativa were found to be 49.3 and 54.3% at Kappa number of 29, respectively. An anthraquinone (AQ) dose of 0.1% increases the pulp yield to the tune of around 0.6% as well reduce the Kappa number to the tune of 22%. CEHH bleaching of C. sativa produces pulp brightness of 82% (Elrepho) at total chlorine demand of 5.07%. On contrary to this the I. carnea kraft pulp at same chlorine demand produce a pulp with improved brightness of 85.4% (Elrepho).     

Quality characteristics and field performance of selectable marker-free transgenic rice with antisense Wx gene and improved quality derived from the elite parents of hybrid indica rice

In rice grains, high amylose content (AC) is correlated with poor grain quality, particularly in indica hybrid rice. To obtain indica hybrid rice with improved cooking and eating qualities, we introduced the antisense Waxy (Wx) gene into 2 elite parental lines of indica hybrid rice by using co-transformation methods. Subsequently, we selected several elite homozygous transgenic lines that did not contain the selectable marker. The expression of the endogenous Wx gene of the selected transgenic lines was significantly downregulated, resulting in low AC in the mature seeds; moreover, the AC in some lines reduced to the level observed in glutinous rice. With the decrease in AC, the gel consistency of the transgenic rice became softer, and the gelatinization temperature tended to be higher than those of the wild types, especially in the case of the Longtefu-derived transformants. We also analyzed the pasting properties of the selected transgenic low-AC lines, and we noted an improvement in the pasting properties of the transgenic rice lines. The results from a field trial indicated that the grain weights of the transgenic lines with lower AC exhibit remarkable reduction compared with those of the wild types.     

58份鲜食玉米品种对瘤黑粉病和丝黑穗病的抗性评价

2020-2022年通过田间人工接种,对58份鲜食玉米品种进行抗性鉴定和评价,明确玉米品种对瘤黑粉病和丝黑穗病的抗性差异。结果表明,58份鲜食玉米中未检测出高抗(HR)瘤黑粉病品种,1份品种原玉糯999表现抗病(R),占比1.7%;福甜73、白甜糯3号、白玉糯2020、甘糯2020等4份材料表现中抗(MR),占比6.9%;27份品种表现感病(S),占比46.6%;26份品种表现高感(HS),占比44.8%。对丝黑穗病鉴定结果表明,未发现高抗(HR)和抗病(R)品种,仅1份品种永糯321表现中抗(MR);其余20份和37份材料分别表现感病(S)和高感(HS),分别占鉴定材料的34.5%和63.8%。