Identification and characterization of large-effect quantitative trait loci for grain yield under lowland drought stress in rice using bulk-segregant analysis

An F_4:5 population of 490 recombinant inbred lines (RILs) from the cross Apo/^2*Swarna was used to detect quantitative trait loci (QTL) with large effects on grain yield under drought stress using bulk-segregant analysis (BSA). Swarna is an important rainfed lowland rice variety grown on millions of hectares in Asia, but is highly susceptible to drought and aerobic soil conditions. Apo is an aerobic-adapted variety with moderate tolerance to drought. Two rice microsatellite (RM) markers, RM324, and RM416, located on chromosomes 2 and 3, respectively, were shown via BSA to be strongly associated with yield under lowland drought stress. The effects of these QTL were tested in a total of eight hydrological environments over a period of 3 years. The QTL linked to RM416 (DTY _3.1 ) had a large effect on grain yield under severe lowland drought stress, explaining about 31% of genetic variance for the trait (P < 0.0001). It also explained considerable variance for yield under mild stress in lowland conditions and aerobic environments. To our knowledge this is the first reported QTL that has a large effect on yield in both lowland drought and aerobic environments. The QTL linked to RM324 (DTY _2.1 ) had a highly significant effect on grain yield in lowland drought stress (R ² = 13–16%) and in two aerobic trials. The effect of these QTL on grain yield was verified to be not mainly due to phenology differences. Effects of DTY _3.1 on yield under stress have been observed in several other rice mapping populations studied at IRRI. Results of this study indicate that BSA is an effective method of identifying QTL alleles with large effects on rice yield under severe drought stress. The Apo alleles for these large-effect QTL for grain yield under drought and aerobic conditions may be immediately exploited in marker-assisted-breeding to improve the drought tolerance of Swarna.     

A large-effect QTL for rice grain yield under upland drought stress on chromosome 1

Drought is a major abiotic stress factor limiting rice production in rainfed areas. In this study we identified a large-effect quantitative trait locus (QTL) associated with grain yield under stress in five different populations on chromosome 1. The effect of this QTL was further confirmed and characterized in five backcross populations in a total of sixteen stress and non-stress trials during 2006 and 2008. In all the stress trials (eight in total) qDTY1.1 showed strong association with grain yield explaining on average 58% of the genetic variation in the trait. Homozygotes for the tolerant parent allele (Apo) yielded on average 27% more than the susceptible parent allele (IR64) homozygotes. Using an Apo/^3*IR64 population, the peak of this QTL (qDTY1.1) was mapped to an interval between RM486 and RM472 at 162.8?cM at a LOD score of 9.26. qDTY1.1 was strongly associated with plant height in all the environments; this was probably due to the presence of the sd1 locus in this genomic region. In a Vandana/^3*IR64 population segregating for sd1, a strong relation between plant height and yield under stress was observed. The observed relation between increased height and drought tolerance is likely due to tight linkage between qDTY1.1 and sd1 and not due to pleiotrophy of sd1. Thus there is a possibility of combining reduced plant height and drought tolerance in rice. The large and consistent effect of qDTY1.1 across several genetic backgrounds and environments makes it a potential strong candidate for use in molecular breeding of rice for drought tolerance.     

Increased drought tolerance and wider adaptability of qDTY 12.1 conferred by its interaction with qDTY 2.3 and qDTY 3.2

The genetic basis of high grain yield under reproductive-stage drought was studied using an F3-derived population generated from the cross of upland rice (Oryza sativa L.) cultivars Vandana and Way Rarem. Contributed by the susceptible parent Way Rarem, locus qDTY _12.1 was hypothesized to have interaction with loci from the Vandana genome to enhance the grain yield of tolerant line Vandana under drought. A test of the digenic interaction of qDTY _12.1 showed that two loci, qDTY _2.3 on chromosome 2 and qDTY _3.2 on chromosome 3, significantly increased the yield and harvest index of qDTY _12.1 -positive lines under severe upland and lowland drought conditions. qDTY _2.3 and qDTY _3.2 , in interaction with qDTY _12.1 , reduced days to flowering and plant height of qDTY _12.1 -positive lines under stress and non-stress conditions in upland. BC2F3-derived backcross inbred lines (BILs) were used to validate these results and identify new quantitative trait loci. Lines with qDTY _2.3 and qDTY _12.1 showed increased yield over Way Rarem under severe and moderate stress conditions, in upland. IR84996-50-4-B-4, a selection from one of the BILs, yielded more than the popular drought-tolerant cultivars Apo, UPLRi7, and IR74371-54-1-1 under severe stress conditions. Introgressed segments from Vandana also improved yield under non-stress conditions. The results indicate that digenic interactions can explain the genetic control of complex quantitative traits such as grain yield under drought, and a few interacting loci with large effects on grain yield or yield-related traits may enhance drought response across a wide range of genetic backgrounds and environments when introgressed together.     

Crop performance, nitrogen and water use in flooded and aerobic rice

Irrigated aerobic rice is a new system being developed for lowland areas with water shortage and for favorable upland areas with access to supplementary irrigation. It entails the cultivation of nutrient-responsive cultivars in nonsaturated soil with sufficient external inputs to reach yields of 70–80% of high-input flooded rice. To obtain insights into crop performance, water use, and N use of aerobic rice, a field experiment was conducted in the dry seasons of 2002 and 2003 in the Philippines. Cultivar Apo was grown under flooded and aerobic conditions at 0 and at 150 kg fertilizer N ha^–1. The aerobic fields were flush irrigated when the soil water potential at 15-cm depth reached –30 kPa. A ¹⁵N isotope study was carried out in microplots within the 150-N plots to determine the fate of applied N. The yield under aerobic conditions with 150 kg N ha^–1 was 6.3 t ha^–1 in 2002 and 4.2 t ha^–1 in 2003, and the irrigation water input was 778 mm in 2002 and 826 mm in 2003. Compared with flooded conditions, the yield was 15 and 39% lower, and the irrigation water use 36 and 41% lower in aerobic plots in 2002 and 2003, respectively. N content at 150 kg N ha^–1 in leaves and total plant was nearly the same for aerobic and flooded conditions, indicating that crop growth under aerobic conditions was limited by water deficit and not by N deficit. Under aerobic conditions, average fertilizer N recovery was 22% in both the main field and the microplot, whereas under flooded conditions, it was 49% in the main field and 36% in the microplot. Under both flooded and aerobic conditions, the fraction of ¹⁵N that was determined in the soil after the growing season was 23%. Since nitrate contents in leachate water were negligible, we hypothesized that the N unaccounted for were gaseous losses. The N unaccounted for was higher under aerobic conditions than under flooded conditions. For aerobic rice, trials are suggested for optimizing dose and timing of N fertilizer. Also further improvements in water regime should be made to reduce crop water stress.     

From Flooded to Aerobic Conditions in Rice Cultivation: Consequences for Zinc Uptake

Scarcity of water causes a shift from flooded to aerobic conditions for rice production in zinc deficient areas in Northern China. This shift alters soil conditions that affect zinc availability to the crop. This paper concerns the effect of aerobic compared to flooded conditions on crop biomass production, grain yield and zinc content. A field experiment was done with six rice genotypes (Oryza sativa L.) grown on a calcareous soil, both with (23 kg Zn ha⁻¹) and without Zn fertilization. Sampling was conducted at tillering and physiological mature stage. Zn concentration in the shoots was significantly lower at both stages in plants grown in the aerobic field. At maturity, Zn uptake, biomass production, grain yield and Zn-harvest index [grain Zn/(shoot + grain Zn)] were lower under aerobic cultivation. Rice genotypes including aerobic rice and lowland rice differ in degree of response to low Zn supply. A twofold difference was found among aerobic genotypes in grain yield and Zn uptake. Also Zn-harvest index varied significantly. Zn application affected neither grain yield nor grain Zn content, although it significantly improved biomass production in both systems in most genotypes. These results demonstrate that introduction of aerobic rice systems on calcareous soils may increase Zn deficiency problems.     

Tolerance to Zinc Deficiency in Rice Correlates with Zinc Uptake and Translocation

To study variation in zinc efficiency (ZE) among current Chinese rice genotypes, a pot experiment was conducted with 15 aerobic and 8 lowland rice genotypes. Aerobic rice is currently bred by crossing lowland with upland rice genotypes, for growth in an aerobic cultivation system, which is saving water and producing high yields. A Zn deficient clay soil was used in our screening. Zn deficiency resulted in a marked decrease in shoot dry matter production of most genotypes after 28 days of growth. Genotypes were ranked according to their tolerance to Zn deficiency based on ZE, expressed as the ratio of shoot dry weight at Zn deficiency over that at adequate Zn supply. Substantial genotypic variation in ZE (50–98%) was found among both lowland and aerobic genotypes. ZE correlated significantly (P < 0.05) with Zn uptake (R ² = 0.34), Zn translocation from root to shoot (R ² = 0.19) and shoot Zn concentration (R ² = 0.27). The correlation with seed Zn content was insignificant. In stepwise multiple regression analyses, variation in Zn uptake and Zn translocation explained 53% of variation in ZE. Variation in Zn uptake could be explained only for 32% by root surface area. These results indicate that Zn uptake may be an important determinant of ZE and that mechanisms other than root surface area are of major importance in determining Zn uptake by rice.     

Physiological characterization and allelic diversity of selected drought tolerant traditional rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.) landraces of Koraput,India

Water-deficit stress tolerance in rice is important for maintaining stable yield, especially under rain-fed ecosystem. After a thorough drought-tolerance screening of more than 130 rice genotypes from various regions of Koraput in our previous study, six rice landraces were selected for drought tolerance capacity. These six rice landraces were further used for detailed physiological and molecular assessment under control and simulated drought stress conditions. After imposing various levels of drought stress, leaf photosynthetic rate (P_N), photochemical efficiency of photosystem II (Fv/Fm), SPAD chlorophyll index, membrane stability index and relative water content were found comparable with the drought-tolerant check variety (N22). Compared to the drought-susceptible variety IR64, significant positive attributes and varietal differences were observed for all the above physiological parameters in drought-tolerant landraces. Genetic diversity among the studied rice landraces was assessed using 19 previously reported drought tolerance trait linked SSR markers. A total of 50 alleles with an average of 2.6 per locus were detected at the loci of the 19 markers across studied rice genotypes. The Nei’s genetic diversity (He) and the polymorphism information content (PIC) ranged from 0.0 to 0.767 and 0.0 to 0.718, respectively. Seven SSR loci, such as RM324, RM19367, RM72, RM246, RM3549, RM566 and RM515, showed the highest PIC values and are thus, useful in assessing the genetic diversity of studied rice lines for drought tolerance. Based on the result, two rice landraces (Pandkagura and Mugudi) showed the highest similarity index with tolerant check variety. However, three rice landraces (Kalajeera, Machhakanta and Haldichudi) are more diverse and showed highest genetic distance with N22. These landraces can be considered as the potential genetic resources for drought breeding program.     

Allele mining for a drought responsive gene DRO1 determining root growth angle in donors of drought tolerance in rice (Oryza sativa L.)

Deeper Rooting 1 (DRO1) gene identified from a major QTL on chromosome 9 increases the root growth angle (RGA) and thus facilitates survival under drought and hence is an excellent candidate for rice improvement. Twenty-four major Indian upland and lowland genotypes including the ‘yield under drought’ (DTY) QTL donors were subjected to allele mining of DRO1 (3058 bp) using four pairs of overlapping primers. A total of 216 and 52 SNPs were identified across all genotypes in the gene and coding region (756 bp) respectively with transversions 3.6 fold more common than transitions in the gene and 2.5 times in the CDS. In 251 amino acid long protein, substitutions were found in 19 positions, wherein change in position 92 was the most frequent. Based on allele mining, the 24 genotypes can be classified into 16 primary structure variants ranging from complete functional allele (Satti, IR36 and DTY 3.1 donor, IR81896-B-B-195) to truncated non-functional alleles in PMK2, IR64, IR20 and Swarna. All the DTY donors, other than IR81896-B-B-195, and most of the upland drought tolerant cultivars (Nagina 22, Vandana and Dhagaddeshi) had accumulated 6–19 SNPs and 4–8 amino acid substitutions resulting in substantial differences in their protein structure. The expression analysis revealed that all the genotypes showed upregulation under drought stress though the degree of upregulation varied among genotypes. The information on structural variations in DRO1 gene will be very useful for the breeders, especially in the light of recent breeding programmes on improving drought tolerance using several DTY donors and upland accessions.Supplementary InformationThe online version of this article (10.1007/s12298-021-00950-2).     

Genetic Dissection of Epistatic Interactions Contributing Grain Yield Variability in Rice under Drought

AimsThe aim of the present study was to evaluate the performance of ‘high’-‘low’ yielding pyramided lines (PLs), having the same combinations of qDTYs in Samba Mahsuri, MR219 and IR64-Sub1 genetic backgrounds, and to understand the genetic interactions among QTL and/with genetic background affecting grain yield.BackgroundEpistasis regulates the expression of traits governed by several major/minor genes/QTL. Multiple pyramided lines (PLs) with the same grain yield QTL (qDTYs) combinations but possessing grain yield variability under different levels of reproductive stage drought stress were identified in different rice genetic backgrounds at International Rice Research Institute (IRRI).ObjectivesThe objectives of the present study were to evaluate the performance pyramided lines (PLs) with drought QTL in the backgrounds of Samba Mahsuri, MR219 and IR64-Sub1 under reproductive stage drought stress (RS) and NS (non-stress) conditions, to understand the effect of epistatic interactions among qDTYs and with genetic background on GY under the differential level of stress and to identify the promising drought-tolerant lines with high yield under drought and higher background recovery in different genetic backgrounds.MethodsThe experiments were conducted in 2015 DS (dry season), 2015 WS (wet season) and 2017 DS at IRRI, Los Baños, Philippines, in a transplanted lowland ecosystem under lowland severe stress (LSS), lowland moderate stress (LMS) and lowland non-stress (LNS). The experiments were laid out in alpha lattice design with two replications.ResultsSeveral digenic interactions were found in different genetic backgrounds, 13 interactions in Samba Mahsuri, 11 in MR219 and 20 in IR64-Sub1 backgrounds. Among all digenic interactions, one QTL × QTL interaction, 17 QTL × background and 26 background × background interactions resulted in GY reduction in low yielding PLs in different genetic backgrounds under LSS or LMS. Negative interaction of qDTY_3.1, qDTY_4.1 and qDTY_9.1 with background markers and background × background interactions caused up to 15% GY reduction compared to the high yielding PLs under LMS in the Samba Mahsuri PLs. In MR219 PLs, the negative interaction of qDTY_2.2, qDTY_3.2, qDTY_4.1 and qDTY_12.1 with the background marker interval RM314-RM539, RM273-RM349 and RM445-RM346, RM473D-RM16, respectively resulted 52% GY reduction compared to the high yielding PLs under LSS. In IR64-Sub1 PLs, qDTY_6.1 interacted with background loci at RM16-RM135, RM228-RM333, RM202-RM287 and RM415-RM558A marker interval under LSS and at RM475-RM525 marker interval under LMS, causing GY reduction to 58% compared to the high yielding PLs.ConclusionHigh yielding PLs in Samba Mahsuri (IR 99734:1-33-69-1-22-6), MR219 (IR 99784-156-87-2-4-1) and IR64-Sub1 (IR 102784:2-89-632-2-1-2) backgrounds without any negative interactions were identified. The identified selected promising PLs may be used as potential drought-tolerant donors or may be released as varieties for drought-prone ecosystems in different countries.     

Identification of flanking SSR markers for a major rice gall midge resistance gene <Emphasis Type="Italic">Gm1</Emphasis> and their validation

Host-plant resistance is the preferred strategy for management of Asian rice gall midge (Orseolia oryzae), a serious pest in many rice-growing countries. The deployment of molecular markers linked to gall midge resistance genes in breeding programmes can accelerate the development of resistant cultivars. In the present study, we have tagged and mapped a dominant gall midge resistance gene, Gm1, from the Oryza sativa cv. W1263 on chromosome 9, using SSR markers. A progeny-tested F₂ mapping population derived from the cross W1263/TN1 was used for analysis. To map the gene locus, initially a subset of the F₂ mapping population consisting of 20 homozygous resistant and susceptible lines each was screened with 63 parental polymorphic SSR markers. The SSR markers RM316, RM444 and RM219, located on chromosome 9, are linked to Gm1 at genetic distances of 8.0, 4.9 and 5.9 cM, respectively, and flank the gene locus. Further, gene/marker order was also determined. The utility of the co-segregating SSR markers was tested in a backcross population derived from the cross Swarna/W1263//Swarna, and allelic profiles of these markers were analysed in a set of donor rice genotypes possessing Gm1 and in a few gall midge-susceptible, elite rice varieties.     

Mapping of a wide compatibility locus in indica rice using SSR markers

Hybrid sterility between indica and japonica subspecies in rice is basically caused by partial abortion of gametes and hybrid fertility could be recovered by a single wide compatibility (WC) allele. In this study, a typical indica germplasm source of rice, UPRI 95-162, with strong wide compatibility in cross with japonica rice was studied for location of its WC locus. Bulked segregant analysis was performed and SSRs (simple sequence repeats) were conducted on a F₁ population derived from a three-way cross (UPRI 95-162/T8//Akihikari). The locus was located on chromosome 1 approximately 0.2 cM to SSR markers RM581 on one side and 1.5 cM to RM292 on another. This WC locus, tentatively designated as S-20 ⁿ (t), and its tight linkage markers, RM581 and RM292, would be very useful for efficient marker-assisted selection for breeding new WC varieties and for map-based cloning of the gene.     

Validation and dissection of quantitative trait loci for leaf traits in interval RM4923-RM402 on the short arm of rice chromosome 6

Validation and dissection of a QTL region for leaf traits in rice which has been reported in a number of independent studies were conducted. Three sets of near isogenic lines (NILs) were originated from a residual heterozygous line derived the indica cross Zhenshan 97B/Milyang 46. They were overlapping and totally covered a 4.2-Mb heterogenous region extending from RM4923 to RM402 on the short arm of rice chromosome 6. Each NIL set consisted of 10 maternal lines and 10 paternal lines. They were measured for the length, width, perimeter and area of the top three leaves and the number of spikelets per panicle, number of grains per panicle and grain weight per panicle. In NIL sets 6-4 and 6-7, differing in intervals RM4923-RM225 and RM19410-RM6119, respectively, significant variations with the enhancing alleles from the female parent ZS97 were shown for the length, perimeter and area except for the area of the third leaf from top in 6-4, but the effects were lower in 6-4 than in 6-7. No significant effects were detected for the three traits in the remaining NIL set. It was shown that flag leaf length (FLL) is the primary target of the QTLs detected. Two QTLs for FLL linked in repulsion phase were resolved, of which qFLL6.2 located in the 1.19-Mb interval RM3414-RM6917 had a major effect with the enhancing allele from Zhenshan 97B, and qFLL6.1 located in the 946.8-kb interval RM19350-RM19410 had a smaller effect with the enhancing allele from Milyang 46. The two QTLs also exerted pleiotropic effects on the yield traits.     

A marker-assisted backcross approach for developing submergence-tolerant rice cultivars

Submergence stress regularly affects 15 million hectares or more of rainfed lowland rice areas in South and Southeast Asia. A major QTL on chromosome 9, Sub1, has provided the opportunity to apply marker assisted backcrossing (MAB) to develop submergence tolerant versions of rice cultivars that are widely grown in the region. In the present study, molecular markers that were tightly linked with Sub1, flanking Sub1, and unlinked to Sub1 were used to apply foreground, recombinant, and background selection, respectively, in backcrosses between a submergence-tolerant donor and the widely grown recurrent parent Swarna. By the BC₂F₂ generation a submergence tolerant plant was identified that possessed Swarna type simple sequence repeat (SSR) alleles on all fragments analyzed except the tip segment of rice chromosome 9 that possessed the Sub1 locus. A BC₃F₂ double recombinant plant was identified that was homozygous for all Swarna type alleles except for an approximately 2.3–3.4 Mb region surrounding the Sub1 locus. The results showed that the mega variety Swarna could be efficiently converted to a submergence tolerant variety in three backcross generations, involving a time of two to three years. Polymorphic markers for foreground and recombinant selection were identified for four other mega varieties to develop a wider range of submergence tolerant varieties to meet the needs of farmers in the flood-prone regions. This approach demonstrates the effective use of marker assisted selection for a major QTL in a molecular breeding program. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Host response of rice genotypes to the rice root-knot nematode (Meloidogyne graminicola) under aerobic soil conditions

Aerobic rice is a production system where adapted rice varieties are established via direct seeding in non-puddled, non-flooded, non-saturated fields and grown under conditions similar to upland conditions. On land cultivated continuously with aerobic rice, a yield reduction has been observed. The rice root-knot nematode Meloidogyne graminicola is considered one of the possible causes of these yield reductions. Resistance to and tolerance for M. graminicola are essential traits for aerobic rice cultivars in alleviating this problem. In our study, the host response of nineteen aerobic, seven upland and four lowland rice genotypes which are either being used in the International Rice Research Institute’s aerobic rice breeding programme or already cultivated by farmers in Asia was evaluated under aerobic soil conditions in an outdoor raised-bed experiment. Our study showed a large variation in susceptibility and sensitivity to M. graminicola infection among the rice genotypes examined. Resistance comparable to the resistant reference genotypes included in the experiment (CG14, TOG5674, TOG7235) was not found but in terms of susceptibility, the upland genotype Morobereken may be an interesting less-susceptible genotype. Tolerance was found and in terms of sensitivity, the high yielding aerobic genotype IR78877-208-B-1-2 may be an interesting tolerant genotype. Our study also allowed the identification of rice genotypes that are either highly susceptible or sensitive to M. graminicola infection and of which the cultivation should be discouraged. On average, M. graminicola caused an almost 30% reduction in yield. Excluding the two susceptible and three resistant reference genotypes included in the experiment, most affected was dry-shoot biomass (23.6% reduction) followed by root length, which was more affected than fresh-root weight (19.8 vs. 8%) and grain filling (17.3%), while plant height and the number of spikelets/panicle were less affected (10.2 and 8.1%, respectively). Neither tillering nor the number of panicles/plant were affected.     

Identification of simple sequence repeat markers for utilizing wide-compatibility genes in inter-subspecific hybrids in rice (Oryza sativa L.)

Although pronounced heterosis in inter-subspecific hybrids was known in rice for a long time, its utilization for hybrid rice breeding has been limited due to their hybrid sterility (HS). For the last two decades, however, a few inter-subspecific hybrids have been developed by incorporating wide-compatibility genes (WCG) that resolve HS, into parental lines of these inter-subspecific hybrids. For effective use of WCG, it is necessary to find convenient markers linked to WCG of practical importance. In this paper, initially a set of simple sequence repeat (SSR) markers in the vicinity of known WCG loci identified based on comparative linkage maps have been surveyed in a population derived from the three-way cross- IR36/Dular//Akihikari, where a known donor of WCG Dular was crossed to a representative indica and japonica cultivar. Of the five parental polymorphic markers, RM253 and RM276 were found to be closely linked to the WCG locus S5 at a distance of 3.0 and 2.8 cM, respectively. Later, loci for HS were examined in three F₂ populations derived from inter-subspecific crosses, with same set of SSR markers. The locus S8 was confirmed to have major influence on HS in the F₂ population derived from CHMRF-1/Taichung65 since two SSR markers in its vicinity, RM412 and RM141, co-segregated with HS at a map distance of 7.6 and 4.8 cM, respectively. In the F₂ population derived from the cross BPT5204/Taipei309, three SSR markers in the vicinity of S5, RM50, RM276 and RM136 co-segregated with HS at a map distance of 4.2, 3.2 and 7.8 cM, respectively. In the third F₂ population derived from Swarna/Taipei309, the SSR markers in the vicinity of S5, RM225, RM253, RM50, RM276 and RM136 were identified to co-segregate with HS at a map distance of 3.2, 2.6, 3.4, 2.6 and 6.6 cM, respectively. These results indicated a clear picture of WCG in Dular as well as the predominant role of HS alleles at S5 locus. The identified SSR markers are expected to be used for incorporation of WCG into parental lines in hybrid rice breeding to solve HS in inter-subspecific hybrids.S.P. Singh , R.M. Sundaram contributed equally     

The Photosynthetic Efficiency of Some Elite Rice Hybrids and Restorers

At the vegetative growth stage (40 d), the mean photosynthetic rate (PN) and canopy photosynthesis (PN × LAI) in F1 hybrids and their parents were similar, whereas the maintenance respiration rate (RM) was considerably higher and PN/RM lower in the F1 hybrids than in the parents. Yet at the flowering stage, the hybrids showed higher PN and PN × LAI values, while RM and PN/RM were similar in both. A specific F1 hybrid like IR 62829A×Vajram showed high readings in PN, PN/RM, and PN × LAI at the flowering stage, while IR 62829A×Swarna followed by IR 62829A×Vajram had high values 40 d after planting. The parents Swarna and Vajram, although moderate in PN, had the highest PN × LAI at the flowering stage due to a greater LAI.     

Fine Mapping QTL for Drought Resistance Traits in Rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.) Using Bulk Segregant Analysis

Drought stress is a major limitation to rice (Oryza sativa L.) yields and its stability, especially in rainfed conditions. Developing rice cultivars with inherent capacity to withstand drought stress would improve rainfed rice production. Mapping quantitative trait loci (QTLs) linked to drought resistance traits will help to develop rice cultivars suitable for water-limited environments through molecular marker-assisted selection (MAS) strategy. However, QTL mapping is usually carried out by genotyping large number of progenies, which is labour-intensive, time-consuming and cost-ineffective. Bulk segregant analysis (BSA) serves as an affordable strategy for mapping large effect QTLs by genotyping only the extreme phenotypes instead of the entire mapping population. We have previously mapped a QTL linked to leaf rolling and leaf drying in recombinant inbred (RI) lines derived from two locally adapted indica rice ecotypes viz., IR20/Nootripathu using BSA. Fine mapping the QTL will facilitate its application in MAS. BSA was done by bulking DNA of 10 drought-resistant and 12 drought-sensitive RI lines. Out of 343 rice microsatellites markers genotyped, RM8085 co-segregated among the RI lines constituting the respective bulks. RM8085 was mapped in the middle of the QTL region on chromosome 1 previously identified in these RI lines thus reducing the QTL interval from 7.9 to 3.8 cM. Further, the study showed that the region, RM212–RM302–RM8085–RM3825 on chromosome 1, harbours large effect QTLs for drought-resistance traits across several genetic backgrounds in rice. Thus, the QTL may be useful for drought resistance improvement in rice through MAS and map-based cloning.     

Erratum to: Development and application of gene-based markers for the major rice QTL Phosphorus uptake 1

Marker-assisted breeding is a very useful tool for breeders but still lags behind its potential because information on the effect of quantitative trait loci (QTLs) in different genetic backgrounds and ideal molecular markers are unavailable. Here, we report on some first steps toward the validation and application of the major rice QTL Phosphate uptake 1 (Pup1) that confers tolerance of phosphorus (P) deficiency in rice (Oryza sativa L.). Based on the Pup1 genomic sequence of the tolerant donor variety Kasalath that recently became available, markers were designed that target (1) putative genes that are partially conserved in the Nipponbare reference genome and (2) Kasalath-specific genes that are located in a large insertion-deletion (INDEL) region that is absent in Nipponbare. Testing these markers in 159 diverse rice accessions confirmed their diagnostic value across genotypes and showed that Pup1 is present in more than 50% of rice accessions adapted to stress-prone environments, whereas it was detected in only about 10% of the analyzed irrigated/lowland varieties. Furthermore, the Pup1 locus was detected in more than 80% of the analyzed drought-tolerant rice breeding lines, suggesting that breeders are unknowingly selecting for Pup1. A hydroponics experiment revealed genotypic differences in the response to P deficiency between upland and irrigated varieties but confirmed that root elongation is independent of Pup1. Contrasting Pup1 near-isogenic lines (NILs) were subsequently grown in two different P-deficient soils and environments. Under the applied aerobic growth conditions, NILs with the Pup1 locus maintained significantly higher grain weight plant⁻¹ under P deprivation in comparison with intolerant sister lines without Pup1. Overall, the data provide evidence that Pup1 has the potential to improve yield in P-deficient and/or drought-prone environments and in diverse genetic backgrounds.     

Fine-mapping of qRL6.1, a major QTL for root length of rice seedlings grown under a wide range of NH4 + concentrations in hydroponic conditions

Root system development is an important target for improving yield in cereal crops. Active root systems that can take up nutrients more efficiently are essential for enhancing grain yield. In this study, we attempted to identify quantitative trait loci (QTL) involved in root system development by measuring root length of rice seedlings grown in hydroponic culture. Reliable growth conditions for estimating the root length were first established to renew nutrient solutions daily and supply NH₄ ⁺ as a single nitrogen source. Thirty-eight chromosome segment substitution lines derived from a cross between ‘Koshihikari’, a japonica variety, and ‘Kasalath’, an indica variety, were used to detect QTL for seminal root length of seedlings grown in 5 or 500 μM NH₄ ⁺. Eight chromosomal regions were found to be involved in root elongation. Among them, the most effective QTL was detected on a ‘Kasalath’ segment of SL-218, which was localized to the long-arm of chromosome 6. The ‘Kasalath’ allele at this QTL, qRL6.1, greatly promoted root elongation under all NH₄ ⁺ concentrations tested. The genetic effect of this QTL was confirmed by analysis of the near-isogenic line (NIL) qRL6.1. The seminal root length of the NIL was 13.5–21.1% longer than that of ‘Koshihikari’ under different NH₄ ⁺ concentrations. Toward our goal of applying qRL6.1 in a molecular breeding program to enhance rice yield, a candidate genomic region of qRL6.1 was delimited within a 337 kb region in the ‘Nipponbare’ genome by means of progeny testing of F₂ plants/F₃ lines derived from a cross between SL-218 and ‘Koshihikari’.     

Fine mapping of <Emphasis Type="Italic">Sta1</Emphasis>, a quantitative trait locus determining stele transversal area,on rice chromosome 9

The stele (root vascular cylinder) in plants plays an important role in the transport of water and nutrients from the root to the shoot. A quantitative trait locus (QTL) on rice chromosome 9 that controls stele transversal area (STA) was previously detected in an F₃ mapping population derived from a cross between the lowland cultivar ‘IR64’, with a small STA, and the upland cultivar ‘Kinandang Patong’, with a large STA. To identify the gene(s) underlying this QTL, we undertook fine mapping of the locus. We screened eight plants from BC₂F₃ lines in which recombination occurred near the QTL. Progeny testing of BC₂F₄ plants was used to determine the genotype classes for the QTL in each BC₂F₃ line. Accordingly, the STA QTL Sta1 (Stele Transversal Area 1) was mapped between the InDel markers ID07_12 and ID07_14. A candidate genomic region for Sta1 was defined more precisely between markers RM566 and RM24334, which delimit a 359-kb interval in the reference cultivar ‘Nipponbare’. A line homozygous for the ‘Kinandang Patong’ allele of Sta1 had an STA approximately 28.4% larger than that of ‘IR64’. However, Sta1 did not influence maximum or total root length, suggesting that this QTL specifically controls STA.