Changes in juice quality and sugarcane yield with recurrent selection for sucrose

Sugarcane (Saccharum spp. hybrids) breeding programs in Louisiana have made improving sucrose content a top priority because a short growing season limits cane yield. Using a recurrent selection strategy, the cultivars with the highest sucrose content are crossed, and a new generation of cultivars is selected from the progeny. This study was designed to determine how selection primarily for sucrose content has modified physiological characters, and impacted sucrose content and yield. Five cultivars were randomly selected from each of seven generations of recurrent selection in Louisiana and planted in two experiments. The plant and first stubble crops were harvested late in the harvest season from each experiment. Cane yield and juice quality were determined. Cultivars from the last three generations were superior to cultivars from the first three generations for Brix % cane, sucrose % cane, purity, theoretically recoverable sugar (TRS), cane yield and sugar yield. Fiber % cane was not different among the generations. Selection primarily for sucrose has increased Brix % cane from 14% to 16%, sucrose % cane from 12% to 14%, purity from 82.5% to 87.3%, and TRS from 98 to 122 kg Mg⁻¹. A plateau in juice quality and sucrose yield in the last three generations may indicate that: (1) Louisiana's short growing season may restrict sucrose accumulation; (2) the genetic potential for late season juice quality has been reached with currently available germplasm; or (3) the inclusion of lower juice quality Saccharum spontaneum germplasm into the breeding program in order to increase disease tolerance, cold tolerance, and ratooning ability has diluted the effect of recurrent selection for sucrose.     

Integration of Genomics into Rice Breeding

One of the major challenges in genetics has been to identify the nucleotide polymorphisms responsible for phenotypic variation. Through intensive analysis, several major quantitative trait loci (QTLs) for agronomic traits in rice have been identified and the underlying candidate genes have been delimited. Advanced mapping populations, including chromosome segment substitution lines, have enhanced the power of genetic analysis to detect QTL alleles, even those with minor effects. Recent examples of marker-assisted selection have proven the potential of this strategy for crop improvement. The genome-wide discovery of single nucleotide polymorphisms (SNPs), even among closely related cultivars, has enhanced the power of allele mining in a wide range of rice breeding materials. An array-based SNP genotyping system can be used to visualize pedigree haplotypes in breeding materials, including landraces and modern cultivars. All of these technologies are accelerating the genetic dissection of complex agronomic traits and further improvement of rice.     

Improvement of rice drought tolerance through backcross breeding: Evaluation of donors and selection in drought nurseries

A large-scale backcross breeding project has been undertaken to improve drought tolerance in rice. Over 160 donor cultivars from 25 countries have been used in this project, representing a significant proportion of the genetic variation in cultivated rice. These cultivars were evaluated in field experiments in the Philippines to assess their responses to drought in terms of plant height, heading date, and grain yield. Drought was imposed near heading stage, in experiments that were established either in lowland (anaerobic) fields or upland (aerobic) soil. Despite the poor adaptation of some cultivars to the tropics, it was possible to identify significant variation in plant response to drought treatments, and contrasting effects on flowering delay and growth. Subsequently, 325 BC₂F₂ bulk populations, developed by backcrossing many of these donors to one of three elite recurrent parents, were screened under drought in lowland or upland nurseries. Stress levels were managed to eliminate almost all seed set in recurrent parents, and those progeny that produced grain were selected as being putatively drought-tolerant. The selection intensity varied across years and in selection environments with more severe stress, higher selection intensity could be imposed. The number of plants selected within a population was not associated with the per se drought response of the donors in the direct evaluation, indicating the wide presence of cryptic genetic variation for drought tolerance in the apparently drought-susceptible cultivars. The genetic background of the recurrent parent affected the number of plants selected, as did the selection environment (upland versus lowland nurseries). These drought-selected introgression lines represent a useful genetic resource to develop improved cultivars for farmers in rainfed or water-scarce rice-growing regions, and also to improve our understanding of the genetic and molecular basis of drought tolerance in rice. Genetic analysis of the selected lines, reported elsewhere, indicated specific regions of high introgression. Yield evaluations of the selected lines are now underway across a range of drought scenarios.     

Rapid prediction of head rice yield and grain shape for genome-wide association study in indica rice

Rice milling and appearance qualities are the main determinants of market price of the milled rice, so great breeding efforts have been directed to improve the milling and appearance quality. The success of breeding efforts depends on the accurate and rapid phenotyping of the quality traits in early generations. This study was conducted to first validate the effectiveness of the PaddyCheck to measure head rice yield (HRY) and paddy grain length of 40 indica rice cultivars. The results indicated that the PaddyCheck data had positively correlated with the lab methods of HRY (r = 0.81**) and grain length (r = 0.97**). An association panel including 281 indica rice accessions was phenotyped with the PaddyCheck and the data were used for genome-wide association study (GWAS) to identify quantitative trait locus (QTL) for milling and appearance quality. A total of nine QTLs were identified, among which the major genes GS3 and qSW5 were identified for grain length and width, respectively. Furthermore, a novel QTL on short arm of chromosome 6 was identified for HRY. Our study indicated that PaddyCheck measurement was accurate and effective, and could be applied in rice breeding for improvement of grain shape and milling quality. The nine QTLs identified in indica rice could be used in marker assisted selection in rice breeding programs.     

An in planta, Agrobacterium-mediated transient gene expression method for inducing gene silencing in rice (Oryza sativa L.) leaves

Background

Although the genetic structure of rice germplasm has been characterized worldwide, few studies investigated germplasm from Thailand, the world’s largest exporter of rice. Thailand and the International Rice Research Institute (IRRI) have diverse collections of rice germplasm, which could be used to develop breeding lines with desirable traits. This study aimed to investigate the level of genetic diversity and structures of Thai and selected IRRI germplasm. Understanding the genetic structure and relationships among these germplasm will be useful for parent selection used in rice breeding programs.

Results

From the 98 InDel markers tested for single copy and polymorphism, 19 markers were used to evaluate 43 Thai and 57 IRRI germplasm, including improved cultivars, breeding lines, landraces, and 5 other Oryza species. The Thai accessions were selected from all rice ecologies such as irrigated, deep water, upland, and rainfed lowland ecosystems. The IRRI accessions were groups of germplasm having agronomic desirable traits, including temperature-sensitive genetic male sterility (TGMS), new plant type, early flowering, and biotic and abiotic stress resistances. Most of the InDel markers were genes with diverse functions. These markers produced the total of 127 alleles for all loci, with a mean of 6.68 alleles per locus, and a mean Polymorphic Information Content (PIC) of 0.440. Genetic diversity of Thai rice were 0.3665, 0.4479 and 0.3972 for improved cultivars, breeding lines, and landraces, respectively, while genetic diversity of IRRI improved and breeding lines were 0.3272 and 0.2970, respectively. Cluster, structure, and differentiation analyses showed six distinct groups: japonica, TGMS, deep-water, IRRI germplasm, Thai landraces and breeding lines, and other Oryza species.

Conclusions

Thai and IRRI germplasm were significantly different. Thus, they can be used to broaden the genetic base and trait improvements. Cluster, structure, and differentiation analyses showed concordant results having six distinct groups, in agreement with their development, and ecologies.     

Hidden diversity for abiotic and biotic stress tolerances in the primary gene pool of rice revealed by a large backcross breeding program

Low and unstable rice productivity in many areas of Asia is associated with many abiotic and biotic stresses such as drought, salinity, anaerobic conditions during germination, submergence, phosphorus and zinc deficiency, etc. To develop rice varieties with tolerance to these stresses, we undertook a large backcross (BC) breeding effort for the last 6 years, using three recurrent elite rice lines and 203 diverse donors, which represent a significant portion of the genetic diversity in the primary gene pool of rice. Significant progress has been made in the BC breeding program, which resulted in development of large numbers of introgression lines with improved tolerance to these stresses. Promising lines have been developed with excellent tolerances (extreme phenotypes) to salinity, submergence and zinc deficiency; resistance to brown plant hopper, ability to germinate under the anaerobic condition and low temperature. Our results indicated that there exist tremendous amounts of ‘hidden’ diversity for abiotic and biotic stress tolerances in the primary gene pool of rice. Furthermore, we demonstrated that despite the complex genetics and diverse physiological mechanisms underlying the abiotic stress tolerances, introgression of genes from a diverse source of donors into elite genetic backgrounds through BC breeding and efficient selection (careful screening under severe stress) is a powerful way to exploit this hidden diversity for improving abiotic stress tolerances of rice. We have developed three large sets of introgression lines, which not only provide an unique platform of breeding materials for developing new rice cultivars with superior yield and stability by trait/gene pyramiding, but also represent unique genetic stocks for a large-scale discovery of genes/alleles underlying the abiotic and biotic stress tolerances of rice using genomic tools.     

Variance components for yield and specific gravity in a diploid potato population after two cycles of recurrent selection

The potato(Solanum tuberosum L.) processing industry needs cultivars with high tuber specific gravity and acceptable color of processed product. All of the cultivars with high specific gravity currently grown in the U.S. are very closely related, which increases their genetic vulnerability and results in inbreeding as efforts are made to improve these traits. The use of diploidSolanum sp. in breeding may resolve these problems. The purposes of this study were (1) to estimate narrow-sense heritability for yield and specific gravity in random-mating diploid hybrid potato populations ofS. phureja - S. stenotomum (PHU-STN) following two cycles of recurrent selection, (2) to examine phenotypic variances for yield and specific gravity following two cycles of recurrent selection within PHU-STN, (3) to compare the yield and specific gravity of individual PHU-STN clones with Atlantic, and (4) to screen these PHU-STN clones for the presence of 2n pollen. Four clones from each of 72 maternal half-sib families were evaluated for yield and specific gravity in replicated field tests in 1990 and 1991. A second selection cycle, using a randomly mated population obtained from the highest specific gravity clone in each maternal half-sib family, was similarly evaluated for yield and specific gravity in replicated field tests in 1995 and 1996. Narrow-sense heritability for specific gravity was estimated as 0.37 ± 0.25 and 0.43 ± 0.27, in the first and second selection cycles, respectively, with a 27% decrease in phenotypic variance. Narrow-sense heritability for yield was estimated as 0.60 ± 0.26 and 0.06 ± 0.24, in the first and second selection cycles, respectively, with a 73% decrease in phenotypic variance. There were significant correlations between yield and specific gravity in 1990 (r=0.32) and 1996 (r=0.37), but not 1991 (r=0.08) and 1995 (r=0.05). These results indicate that additional breeding efforts in this PHU-STN population could result in improvements in specific gravity. However, the amount of variation for yield in this population is decreasing and may indicate that the yield potential of this population is rapidly approaching its limit. In the second selection cycle, many of the 288 clones were significantly higher in specific gravity than the high-specific-gravity cultivar Atlantic, but none were higher yielding. Fifty-eight clones from the second selection cycle produced at least 5% 2n pollen. When used in tetraploid x diploid hybridizations, this diploid population could furnish new genetic material to the tetraploid potato germplasm base for simultaneously increasing specific gravity and yield.     

A simple method for squeezing juice from rice stems and its use in the high-throughput analysis of sugar content in rice stems

Sugar content in rice (Oryza sativa L.) stem is an agronomically important trait for rice used in straw silage or whole-crop silage. However, the mechanisms underlying sugar accumulation in rice stems remain unclear, mainly due to the time-consuming method for measuring sugar content. Here, we established a simple method for squeezing stem juice from rice plants, similar to that used during breeding selection in sugarcane or sorghum. The Brix value of the stem juice, which can easily be measured using a portable refractometer, significantly correlated with the soluble sugar contents in the stem juice and tended to correlate with those in stem tissues. This indicates that the Brix value of the stem juice can be used for estimating the sugar content in rice stems. This simple estimation method will be a useful tool for high-throughput analysis of sugar content in rice stems during mutant screening, QTL analysis, and breeding selection.     

Genetic Dissection of Grain Size Traits Through Genome-Wide Association Study Based on Genic Markers in Rice

Grain size plays a significant role in rice, starting from affecting yield to consumer preference, which is the driving force for deep investigation and improvement of grain size characters. Quantitative inheritance makes these traits complex to breed on account of several alleles contributing to the complete trait expression. We employed genome-wide association study in an association panel of 88 rice genotypes using 142 new candidate gene based SSR (cgSSR) markers, derived from yield-related candidate genes, with the efficient mixed-model association coupled mixed linear model for dissecting complete genetic control of grain size traits. A total of 10 significant associations were identified for four grain size-related characters (grain weight, grain length, grain width, and length-width ratio). Among the identified associations, seven marker trait associations explain more than 10% of the phenotypic variation, indicating major putative QTLs for respective traits. The allelic variations at genes OsBC1L4, SHO1 and OsD2 showed association between 1000-grain weight and grain width, 1000-grain weight and grain length, and grain width and length-width ratio, respectively. The cgSSR markers, associated with corresponding traits, can be utilized for direct allelic selection, while other significantly associated cgSSRs may be utilized for allelic accumulation in the breeding programs or grain size improvement. The new cgSSR markers associated with grain size related characters have a significant impact on practical plant breeding to increase the number of causative alleles for these traits through marker aided rice breeding programs.     

Mass and line selection can produce equally uniform rice varieties

We compared intra-varietal variation of two rice varieties (Ashoka 200F and Ashoka 900F) produced by a very simple bulk breeding method (mass selection with no line selection at any stage) with one line-selected variety (Ashoka 228), all derived from the same cross. Their parents, the upland variety Kalinga III and the irrigated transplanted medium-lowland variety IR64, both originated through line selection and were used as control varieties.

Panicle-to-row progenies of all the varieties were evaluated in eastern India under irrigation in the dry season and in the rainy season using two water regimes; entirely rainfed or with supplementary irrigation. Intra-varietal variation for quantitative traits, irrespective of the method of breeding, was low. Only Ashoka 200F had significant variation for grain yield, days to flowering and plant height but only in the dry season. This season was not the target of the breeding programme and selection would be unlikely to produce a worthwhile response for the rainy season.

At 43 SSR loci there was more genetic variation between lines within the bulk-selected varieties than within Ashoka 228. Kalinga III was the least variable variety while IR64 had less heterozygosity but greater heterogeneity than the two bulk-selected varieties.

Despite the greater simplicity of the method, mass selection in bulk populations produced varieties that met the distinctness, uniformity and stability (DUS) criteria for seed certification in India. Such uniformity was achieved because of the high selection pressures applied to the bulk. We conclude that this very simple bulk-population breeding approach is highly cost-effective and produces sufficient seed for wide testing earlier than any alternative method.     

Relationships Among Antioxidant Activity, Total Phenolic Content and Specific Gravity in Several Potato (Solanum tuberosum L.) Cultivars Grown in Different Environments

Environmental conditions influence crop productivity and quality, making breeding for improvement of a particular trait challenging. Similarly, relationships among traits may make trait improvement difficult, especially if selection for high levels of one trait results in low levels of the other(s). Therefore, understanding the influence of environment and relationships among traits is necessary in trait selection and crop improvement. The objective of this study was to investigate the variability and correlations among antioxidant activity (AOA), total phenolic content (TP), and specific gravity (SPG) in potato cultivars and advanced breeding selections. This research included investigation of genotype x environment (GxE), using four cultivars (Atlantic, Red LaSoda, Russet Norkotah, and Yukon Gold) grown for 3 years (2005, 2006, and 2007) in nine states (CA, ID, MI, MN, NJ, NC, OR, TX, and WI), and two broader genotype studies using 15 advanced breeding selections grown in Texas in 2005 and 60 advanced selections and five cultivars grown in Texas in 2009. Two methods, 2,2-diphenyl-1-picrylhydrazyl (DPPH) and 2,2′-azinobis(3-ethyl-benzothiazoline-6-sulfonic acid) (ABTS), were used to evaluate AOA, and total phenolic (TP) content was determined using the Folin-Ciocalteau method. Significant effects of cultivar, year, location and their interactions on AOA, TP, and SPG were observed, as well as significant trait differences among cultivars within and between locations. The correlations between AOA and TP were significantly positive, while between AOA and SPG, and between TP and SPG were weak and negative in the GxE study. Correlations between AOA and SPG, and between TP and SPG in the two genotype studies were not significant. The weak relationships observed in the GxE study between AOA and SPG, and between TP and SPG may have been due to the small sample size and/or the cultivar Atlantic consistently exhibiting the lowest values of AOA and TP, and highest SPG in all locations. Results from the genotype studies suggest that breeding for high AOA and TP to increase the nutritional value of potato cultivars can be done without compromising tuber quality in terms of specific gravity.     

黑龙江省水稻新品系品质状况研究

选用16个目前黑龙江省较有希望推广的新品系,种植于省内4个积温带中的典型生态环境地点,初步分析了每个品系的品质表现。主要结果如下:供试材料品质性状除垩白大小外,国优一级达标率为25%以上,而国优二级达标率均在87.5%以上;比较而言,垩白度的降低应是重要育种目标之一;早晚熟品种在综合性状表现上各有优势,早熟品种的整精米率、垩白度、直链淀粉含量占优势;而晚熟品种在胶稠度、食味上占优势。     

Selection indices for improving selection efficiency in Indian mustard

In Indian mustard (Brassica juncea L. Czern & Coss), a major oilseed brassica crop, oil yield is the ultimate trait of economic value, which is determined by seed yield (SY) and oil content (OC). SY, the end product of many complex biological processes, is influenced by many traits, such as plant height (PH), branch number, siliqua number, seed weight, seed size and pod length. It is difficult to accurately select for high-yielding genotypes based exclusively on SY, neglecting other yield-determining traits in commercial breeding programs. Therefore, it is desirable for breeders to simultaneously improve several traits of economic importance, most of which are quantitative in nature. The purpose of the present study was to develop selection indices for simultaneous selection of multiple quantitative traits to enhance selection efficiency of the mustard breeding program of Punjab Agricultural University (PAU) located in Abohar, Punjab. A set of 487 diverse mustard genotypes, comprising germplasm accessions of Indian and European origin, advanced breeding lines, landraces, and cultivars, was evaluated using an alpha lattice design for 2 years (2015–16 and 2016–17) at the Regional Research Station of PAU, Abohar, District Fazilka (the major mustard-growing region of the Punjab state). Data on PH, main shoot length (MSL), number of primary branches (NPB), number of secondary branches (NSB), number of siliquae on main shoot (NSMS), siliqua length (SL), number of seeds per pod (NSP), 1000-seed weight (TSW), SY on a plot basis and OC were recorded. To compute selection indices, economic weights, as determined via path coefficient analysis, were assigned to major yield-determining traits. Out of eight recorded agronomic traits, four traits, viz., NSMS, TSW, NSB and NPB, had larger direct effects on SY than other traits, and hence were assigned relative economic weights of 0.60, 0.20, 0.12 and 0.08, respectively. Selection indices were computed using different combinations of traits via Kang_SASPath computer program. When seven traits were used in a selection index (PH, NPB, NSB, NSMS, SY, TSW and MSL; or PH, NPB, NSB, NSMS, SY, TSW and OC), expected genetic advance (GA)at 5% selection intensity was about the same (9.55; selection efficiency or SE = 163% compared with selection based on SY alone).The GA was 9.46 (SE = 161%)for five traits, viz., NPB, NSB, NSMS, SY and TSW; and 9.30 (SE = 159%)for four traits, viz., NPB, NSB, NSMS, and TSW. These GAs were compared with the GA for SY only, which was 5.90 (benchmark; SE = 100%). We concluded that simultaneous selection based on multiple traits was always more efficient than selection based on SY alone. As there was only a small difference between the GA based on four traits (SE = 161%) and GA based on seven traits (SE = 163%), we suggest that mustard breeders use the parsimonious combination of four traits, viz., NPB, NSB, NSMS, and SY, to enhance SY and, consequently, oil yield in mustard.     

Phenotypic Analyses of Multi-Environment Data for Two Diverse Tetraploid Potato Collections: Comparing an Academic Panel with an Industrial Panel

Phenotypic analyses of two different association panels of tetraploid potato cultivars are presented. Association panels are sets of variously related genotypes assembled for association analysis purposes. The aims of this research were to inspect, analyse and compare two phenotypic data sets, a first step in association mapping analysis. A first panel of 205 contemporary and historical cultivars, selected to represent the commercial potato germplasm pool, was evaluated in two trials in 2006, one on sandy soil and the other on clay soil, both with two replications. It was called the academic panel. Data for the second panel with 299 genotypes were compiled from contributions from five breeding companies and included 66 locations and 18 years. Each of the participating breeding companies contributed data from their clonal selection programmes for 38 advanced breeding clones and a series of standard cultivars. It was called the industrial panel. Variance components for genotypic main effects and genotype-by-environment interactions were calculated, and estimates for the random genotypic main effects were produced. The genotypic main effects for 19 agro-morphological and quality traits were used to study trait by trait correlations within each panel. In addition, for the genotypes shared by both panels, the correlation of genetic main effects between the panels was investigated. The heritability of all traits was high and no large differences were observed between panels. Coefficients of trait variation were highly correlated (r = 0.9) for both panels and trait by trait correlations in both panels showed highly similar patterns. These results demonstrate that a single-year balanced field trial as well as using breeders’ records yields robust phenotypic information that can be used in a genome-wide association study. Issues related to data management and definition of traits are discussed.     

水稻粒形遗传与长粒型优质粳稻育种进展

水稻粒形遗传机制和粒形育种一直是水稻品质和产量研究的重要领域。在粳稻品种选育中,对长粒形遗传种质的选择,已经成为近年来一种新的育种趋势。我们在总结粒长及其相关性状的遗传研究进展和已知粒长相关基因功能的基础上,系统地介绍了南方稻区长粒粳稻的育种历程及其选育策略。同时,对以品种嘉禾218为代表的南方长粒晚粳稻系列品种农艺性状和品质特性进行了比较,在阐明长粒粳稻优质、高产的品种特点的同时,提出长粒晚粳育种中选择粒形、兼顾株型、保产提质的选育思路。     

Low temperature increased the biosynthesis of 2-AP,cooked rice elongation percentage and amylose content percentage in rice

Rice fragrance, cooked rice elongation and amylose content are some of the traits used in determining rice grain quality. 2-acetyl-1-pyrroline (2-AP) is the major compound that is responsible for fragrance in rice.This experiment was conducted with two indica rice cultivars: Meixiangzhan 2 and Xiangyaxiangzhan. Three temperature-controlled chambers: High (32 °C from 06:00 to 17:59 and 26 °C from 18:00 to 05:59), medium (27 °C from 06:00 to 17:59 and 21 °C from 18:00 to 05:59) and low (22 °C from 06:00 to 17:59 and 16 °C from 18:00 to 05:59) were used for the study. At the onset of heading, both cultivars were transferred to the three temperature-controlled chambers. Our results showed that in both cultivars, low temperature growth had the highest 2-AP content, while high temperature growth recorded the lowest 2-AP content. Principal component analysis showed remarkable differences in the metabolomes of rice grown in high, medium and low regimes. In the grains of both cultivars, we observed significant reduction in 2-AP content after 6 and 9 months of storage, however; 2-AP retention differed greatly in both cultivars. We also reported that low temperature growth increased cooked rice elongation percentage and the biosynthesis of amylose in rice. In conclusion, our findings will provide more information to breeders working on the improvement of rice grain quality.     

Identification of novel glutelin subunits and a comparison of glutelin composition between japonica and indica rice (Oryza sativa L.)

Glutelin, a major protein in rice grains, is encoded by a multigene family. However, its protein composition is not well characterised. Here, we identified and characterised two novel glutelin subunits, GluBX and GluC. The individual glutelin subunits of japonica cv. Nipponbare and indica cv. 93-11 rice were analysed using 2-dimensional gel electrophoresis, LC–MS/MS, and Western blotting. Comparison of the glutelin profiles between three japonica and three indica cultivars indicated two distinct subunits (GluA-1 and GluA-3 isomers) and a distinction in the subunit composition (notably GluA-3 and Lys-rich GluB-1 components) of these two subspecies. Sequence alignment revealed different nutritional (Lys residues) and functional (Cys residues) characteristics between the type-A and type-B glutelin subfamilies. We also analysed amino acid and total protein contents of the grains in thirty-five cultivars, and we demonstrated that the Lys-rich glutelin composition of indica cultivars is superior to that of japonica cultivars. The Lys-rich and Cys-poor GluBX subunit is a native protein and is a high nutritional protein in grains. Our combined approaches for the identification of glutelin subunits have revealed the nutritional characteristics of individual subunits in rice, and this knowledge will provide new insights for improving grain quality during rice breeding.     

Genetic analysis and validation of quantitative trait loci associated with reproductive-growth traits and grain yield under drought stress in a doubled haploid line population of rice (Oryza sativa L.)

Drought is a major constraint for rice production and yield stability in rainfed ecosystems, especially when it occurs during the reproductive stage. Combined genetic and physiological analysis of reproductive-growth traits and their effects on yield and yield components under drought stress is important for dissecting the biological bases of drought resistance and for rice yield improvement in water-limited environments. A subset of a doubled haploid (DH) line population of CT9993-5-10-1-M/IR62266-42-6-2 was evaluated for variation in plant water status, phenology, reproductive-growth traits, yield and yield components under reproductive-stage drought stress and irrigated (non-stress) conditions in the field. Since this DH line population was previously used in extensive quantitative trait loci (QTLs) mapping of various drought resistance component traits, we aimed at identifying QTLs for specific reproductive-growth and yield traits and also to validate the consensus QTLs identified earlier in these DH lines using meta-analysis. DH lines showed significant variation for plant water status, reproductive-growth traits, yield and yield components under drought stress. Total dry matter, number of panicles per plant, harvest index, panicle harvest index, panicle fertility, pollen fertility, spikelet fertility and hundred grain weight had significant positive correlations with grain yield under drought stress. A total of 46 QTLs were identified for the various traits under stress and non-stress conditions with phenotypic effect ranging from 9.5 to 35.6% in this study. QTLs for panicle exsertion, peduncle length and pollen fertility, identified for the first time in this study, could be useful in marker-assisted breeding (MAB) for drought resistance in rice. A total of 97 QTLs linked to plant growth, phenology, reproductive-growth traits, yield and its components under non-stress and drought stress, identified in this study as well as from earlier published information, were subjected to meta-analysis. Meta-analysis identified 23 MQTLs linked to plant phenology and production traits under stress conditions. Among them, four MQTLs viz., 1.3 for plant height, 3.1 for days to flowering, 8.1 for days to flowering or delay in flowering and 9.1 for days to flowering are true QTLs. Consensus QTLs for reproductive-growth traits and grain yield under drought stress have been identified on chromosomes 1 and 9 using meta-QTL analysis in these DH lines. These MQTLs associated with reproductive-growth, grain yield and its component traits under drought stress could be useful targets for drought resistance improvement in rice through MAB and/or map-based positional analysis of candidate genes.     

Physiological characterization of introgression lines derived from an indica rice cultivar, IR64, adapted to drought and water-saving irrigation

Water scarcity threatens sustainable rice production in many irrigated areas around the world. To cope with the scarcity, aerobic rice culture has been proposed as a promising water-saving technology. The objective was to elucidate the physiological attributes behind the performance of rice introgression lines in water-saving culture. We evaluated yield potential and physiological adaptation traits to water deficit of BC₃-derived lines with the genetic background of an elite indica cultivar, IR64, in the field and in pot experiments. One line, YTH183, had 26% higher yield than IR64 under non-stress conditions (895 vs. 712 g m⁻² on average). This was attributed to enlarged sink capacity due to large grain size, which contributed to more efficient use of assimilates and hence a higher harvest index. YTH183 also showed better dehydration avoidance under intermittent soil drying, due to the adaptive response of deep rooting to water deficiency. The grain yield of YTH183 exceeded that of IR64 by 92-102% under moderate water deficit caused by limited irrigation in aerobic rice culture (143 vs. 72 g m⁻²). Two introgressed segments on chromosomes 5 and 6 might, at least in part, confer the higher yield potential and greater dehydration avoidance in YTH183 simultaneously. Advanced backcross breeding combined with molecular genetics and physiological characterization of introgressed segments would be effective for developing new rice cultivars with high yield potential and drought adaptation traits.     

Development of elite breeding lines conferring Bph18 gene-derived resistance to brown planthopper (BPH) by marker-assisted selection and genome-wide background analysis in japonica rice (Oryza sativa L.)

Brown planthopper (BPH) is a serious threat to rice production. In this study, we have used the novel resistance gene Bph18 derived from Oryza australiensis and incorporated it into an elite japonica cultivar, Junambyeo, which is highly susceptible to BPH. The Bph18 gene was introduced by marker-assisted backcross (MAB) breeding into Junambyeo. The backcrossed progenies were evaluated for desirable agronomic and grain quality traits and the selection of improved breeding lines while simultaneously evaluating BPH resistance by bioassays in the greenhouse and foreground selection. Of the 26 advanced backcross breeding lines (ABL), four lines showed agronomic traits similar to those of the recurrent parent, with strong resistance to BPH. Molecular genotyping of the four ABL revealed the conversion of genotypes closely resembling the genotype of Junambyeo. The percentage of donor chromosome segments in ABL decreased from 12.3% in the BC₂ to 9.4%, 8.4% and 5.3% in BC₃, BC₄ and BC₅ generations, respectively. ABL retained small sizes of the donor chromosome segments on chromosomes 1, 2, 10, 11 and 12 but the genomes of ABL2, ABL3 and ABL4 were homosequential to the recurrent parent on chromosomes 3, 4, 5, 6, 7 and 9 without donor chromosome segment introgression. The ABL1 and ABL2 retained only some small segments of the donor genome on chromosomes 9 and 8, respectively. Fine structure analysis of the Bph18 flanking region between RM511 and RM1584 markers on chromosome 12 showed a progressive elimination of donor-derived chromosome segments from BC₂ to BC₅ generations. The percentage of O. australiensis derived chromosome segment substitution in the recurrent parent background decreased from 28% of the donor parent to 6.7%, 3.9%, 3.4% and 3.4% in BC₂, BC₃, BC₄ and BC₅ generations, respectively. However, it was revealed that the O. australiensis-derived chromosome segment (1320 kb) in ABL containing the Bph18 gene was consistently maintained irrespective of advances in backcross generations. BPH resistant elite breeding lines with agronomic and grain quality traits similar to those of the recurrent parent were successfully developed by foreground and background analysis in japonica background without linkage drag.