Marker-assisted selection to introgress rice QTLs controlling root traits into an Indian upland rice variety

A marker-assisted back-crossing (MABC) breeding programme was conducted to improve the root morphological traits, and thereby drought tolerance, of the Indian upland rice variety, Kalinga III. This variety, the recurrent parent in the MABC, had not previously been used for quantitative trait locus (QTL) mapping. The donor parent was Azucena, an upland japonica variety from Philippines. Five segments on different chromosomes were targeted for introgression; four segments carried QTLs for improved root morphological traits (root length and thickness) and the fifth carried a recessive QTL for aroma. Some selection was made at non-target regions for recurrent parent alleles. We describe the selection made in three backcross (BC) generations and two further crosses between BC₃ lines to pyramid (stack) all five target segments. Pyramids with four root QTLs were obtained in eight generations, completed in 6 years using 3,000 marker assays in a total of 323 lines. Twenty-two near-isogenic lines (NILs) were evaluated for root traits in five field experiments in Bangalore, India. The target segment on chromosome 9 (RM242-RM201) significantly increased root length under both irrigated and drought stress treatments, confirming that this root length QTL from Azucena functions in a novel genetic background. No significant effects on root length were found at the other four targets. Azucena alleles at the locus RM248 (below the target root QTL on chromosome 7) delayed flowering. Selection for the recurrent parent allele at this locus produced early-flowering NILs that were suited for upland environments in eastern India.     

Development of upland rice introgression lines and identification of QTLs for basal root thickness under different water regimes

Introgression lines (ILs) are valuable materials for identifying quantitative trait loci (QTLs),evaluating genetic interactions,and marker assisted breeding.A set of 430 ILs (BC5F3) containing segments from upland tropical japonica cultivar IRAT109 in a lowland temperate japonica cultivar Yuefu background were developed.One hundred and seventy-six polymorphic markers were used to identify introgressed segments.No segment from IRAT 109 was found in 160 lines.Introgressed segments of the other 270 lines covered 99.1％ of the donor genome.The mean number of introgressed donor segments per individual was 3.3 with an average length of 14.4 cM.QTL analysis was conducted on basal root thickness (BRT) of the 270 ILs grown under irrigated lowland,upland and hydroponic conditions.A total of 22 QTLs affecting BRT were identified,six QTLs (qBRT3.1,qBRT3.2,qBRT6.1,qBRT8.2,qBRT9.1,and qBRT9.2) were consistently expressed under at least two environments (location and water regime),and qBRT7.2 was a new BRT QTL identified under lowland conditions.IL255 containing qBRT9.1 showed an increase of 10.09％ and 7.07％ BRT over cultivar Yuefu when grown under upland and lowland conditions,respectively.Using a population of 304 F2:3 lines derived from the cross IL255 × Yuefu,qBRT9.1 was validated and mapped to a 1.2 cM interval between RM24271 and RM566.The presence of qBRT9.1 explained 12％ of BRT variation.The results provide upland rice ILs and BRT QTLs for analyzing the genetic basis of drought resistance,detecting favorable genes from upland rice,and rice drought resistance breeding.     

Quantitative trait loci for yield and yield components in an Oryza sativa×Oryza rufipogon BC2F2 population evaluated in an upland environment

An advanced backcross breeding strategy was used to identify quantitative trait loci (QTLs) associated with eight agronomic traits in a BC₂F₂ population derived from an interspecific cross between Caiapo, an upland Oryza sativa subsp. japonica rice variety from Brazil, and an accession of Oryza rufipogon from Malaysia. Caiapo is one of the most-widely grown dryland cultivars in Latin America and may be planted as a monoculture or in a multicropping system with pastures. The objectives of this study were: (1) to determine whether trait-enhancing QTLs from O. rufipogon would be detected in 274 BC₂F₂ families grown under the drought-prone, acid soil conditions to which Caiapo was adapted, (2) to compare the performance with and without pasture competition, and (3) to compare putative QTL-containing regions identified in this study with those previously reported for populations adapted to irrigated, low-land conditions. Based on analyses of 125 SSLP and RFLP markers distributed throughout the genome and using single-point, interval, and composite interval mapping, two putative O. rufipogon derived QTLs were detected for yield, 13 for yield components, four for maturity and six for plant height.We conclude that advanced backcross QTL analysis offers a useful germplasm enhancement strategy for the genetic improvement of cultivars adapted to stress-prone environments. Although the phenotypic performance of the wild germplasm would not suggest its value as a breeding parent, it is noteworthy that 56% of the trait-enhancing QTLs identified in this study were derived from O. rufipogon. This figure is similar to the 51% of favorable QTLs derived from the same parent in crosses with a high-yielding hybrid rice cultivar evaluated under irrigated conditions in a previous study. In conclusion, parallel studies in rice using AB-QTL analysis provide increasing evidence that certain regions of the rice genome are likely to harbor genes of interest for plant improvement in multiple environments. Received: 3 September 1999 / Accepted: 16 May 2000     

Mapping QTLs and candidate genes for rice root traits under different water-supply conditions and comparative analysis across three populations

To investigate the genetic factors underlying constitutive and adaptive morphological traits of roots under different water-supply conditions, a recombinant inbred line (RIL) population derived from a cross between the lowland rice variety IR1552 and the upland rice variety Azucena with 249 molecular markers, was used in cylindrical-pot experiments. Eighteen QTLs were detected for seminal root length (SRL), adventitious root number (ARN), and lateral root length (LRL) and lateral root number (LRN) on the seminal root at a soil depth of from 3 to 6 cm under flooding and upland conditions. One identical QTL was detected under both flooding and upland conditions. The relative parameters under the two water-supply conditions were also used for QTL analysis. Five QTLs for upland induced variations in the traits were detected with the positive alleles from Azucena. A comparative analysis was performed for the QTLs detected in this study and those reported from two other populations with Azucena as a parent. Several identical QTLs for root elongation were found across the three populations with positive alleles from Azucena. Candidate genes were screened from ESTs and cDNA-AFLP clones for comparative mapping with the detected QTLs. Two genes for cell expansion, OsEXP2 and endo-1,4--D-glucanase EGase, and four cDNA-AFLP clones from root tissues of Azucena, were mapped on the intervals carrying the QTLs for SRL and LRL under upland conditions, respectively.Communicated by H.C. Becker     

QTL analysis and mapping of pi21, a recessive gene for field resistance to rice blast in Japanese upland rice

Field resistance is defined as the resistance that allows effective control of a parasite under natural field conditions and is durable when exposed to new races of that parasite. To identify the genes for field resistance to rice blast, quantitative trait loci (QTLs) conferring field resistance to rice blast in Japanese upland rice were detected and mapped using RFLP and SSR markers. QTL analysis was carried out in F₄ progeny lines from the cross between Nipponbare (moderately susceptible, lowland) and Owarihatamochi (resistant, upland). Two QTLs were detected on chromosome 4 and one QTL was detected on each of chromosomes 9 and 12. The phenotypic variation explained by each QTL ranged from 7.9 to 45.7% and the four QTLs explained 66.3% of the total phenotypic variation. Backcrossed progeny lines were developed to transfer the QTL with largest effect using the susceptible cultivar Aichiasahi as a recurrent parent. Among 82 F₃ lines derived from the backcross, resistance segregated in the expected ratio of resistant 1 : heterozygous 2 : susceptible 1. The average score for blast resistance measured in the field was 4.2 ± 0.67, 7.5 ± 0.51and 8.2 ± 0.66, for resistant, heterozygous and susceptible groups, respectively. The resistance gene, designated pi21, was mapped on chromosome 4 as a single recessive gene between RFLP marker loci G271 and G317 at a distance of 5.0 cM and 8.5 cM, respectively. The relationship to previously reported major genes and QTLs conferring resistance to blasts, and the significance of marker-assisted selection to improve field resistance, are discussed. Received: 8 June 2000 / Accepted: 24 November 2000     

Yield response to water deficit in an upland rice mapping population: associations among traits and genetic markers

A population of recombinant inbred rice lines from a cross between the upland japonica cultivar Azucena and the upland indica cultivar Bala was evaluated in a series of upland field experiments. Water stress was imposed during the reproductive stage by managed irrigation during the dry season, while control treatments were maintained in aerobic, well-irrigated conditions. Water deficit resulted in a yield reduction of 17 to 50%. The genetic correlation between stress and control yields was quite high when stress was mild, and the heritability of yield was similar in stress and control treatments across both years of this study. Genetic correlations between secondary traits such as leaf rolling and drying and yield under stress varied from high (leaf drying) to insignificant (leaf rolling). Lines with superior yield tended to have fewer panicles and larger grain size than the high-yielding parent, Bala, even though the panicle number was positively correlated with yield and the thousand-grain weight was not associated with yield for the population as a whole. Analysis of quantitative trait loci (QTLs) for yield and yield components allowed the identification of 31 regions associated with growth or yield components. Superior alleles came from either parent. Several of the regions identified had also been reported for root mass at depth or maximum root length in this population in other studies made under controlled environments, and for leaf drying (LD) in field studies. However, the direction of the effect of QTLs was not consistent, which indicates that there was not necessarily a causal relationship between these secondary traits and performance. We conclude that mapping populations can provide novel insights on the actual relationships between yield components and secondary traits in stress and control environments and can allow identification of significant QTLs for yield components under drought stress.Abbreviations DAS Days after sowing - GPP Grains per panicle - QTL Quantitative trait locus - RWC Relative water content - SPP Spikelets per panicle - TGW Thousand-grain weight - VPD Vapor pressure deficit     

QTL mapping of root traits in a doubled haploid population from a cross between upland and lowland japonica rice in three environments

To genetically dissect drought resistance associated with japonica upland rice, we evaluated a doubled haploid (DH) population from a cross between two japonica cultivars for seven root traits under three different growing conditions (upland, lowland and upland in PVC pipe). The traits included basal root thickness (BRT), total root number (RN), maximum root length (MRL), root fresh weight (RFW), root dry weight (RDW), ratio of root fresh weight to shoot fresh weight (RFW/SFW) and ratio of root dry weight to shoot dry weight (RDW/SDW). The BRT was significantly correlated with the index of drought resistance, which was defined as the ratio of yield under the stress of the upland condition to that under the normal lowland condition. A complete genetic linkage map with 165 molecular markers covering 1,535 cM was constructed. Seven additive quantitative trait loci (QTLs) and 15 pairs of epistatic loci for BRT and RN were identified under upland and lowland conditions, and 12 additive QTLs and 17 pairs of epistatic QTLs for BRT, RN, MRL, RFW, RFW/SFW and RDW/SDW were identified under the PVC pipe condition. Four additive QTLs and one pair of epistatic QTLs controlling IDR were also found. These QTLs individually explained up to 25.6% of the phenotypic variance. QTL × environment (Q × E) interactions were detected for all root traits, and the contributions of these interactions ranged from 1.1% to 19.9%. Five co-localized QTLs controlling RFW and RDW, RFW/SFW, RDW/SDW and IDR, BRT and RN, RN, MRL and IDR were found. Four types of QTLs governing BRT and RN were classified by their detection in the upland and lowland conditions. Some common QTLs for root traits across different backgrounds were also revealed. These co-localized QTLs and common QTLs will facilitate marker-assisted selection for root traits in rice breeding programs.     

Genotypic Variation in Root Growth Angle in Rice (Oryza sativa L.) and its Association with Deep Root Development in Upland Fields with Different Water Regimes

Deep root development, which is important for the drought resistance in rice (Oryza sativa L.), is a complex trait combining various root morphologies. The objective of this study was to elucidate genotypic variation in deep root development in relation to morphological indicators such as vertical root distribution and root growth angle. Two experiments were conducted: one on upland fields, and one in pots and fields. In experiment 1, the root systems of six rice cultivars on upland fields were physio-morphologically analyzed under different water regimes (irrigated and intermittent drought conditions during panicle development). In experiment 2, cultivar differences in root growth angles were evaluated with 12 cultivars using the basket method under irrigated conditions. No cultivar × environment interactions were found for total root length or deep root length between irrigated and drought conditions in experiment 1. This suggests that constitutive root growth, which is genetically determined, is important for deep root development under intermittent drought conditions during reproductive stage. Among root traits, the deep root ratio (i.e., deep root weight divided by total root weight) was most closely related to deep root length under both water regimes. This suggested that vertical root distribution constitutively affects deep root length. Significant genotypic variation existed in the nodal root diameter and root growth angle of upland rice in experiment 2. It was considered that genotypes with thick roots allocated more assimilates to deep roots through root growth angles higher to the horizontal plane on upland fields. This is the first report on genotypic variation in the root growth angle of rice on upland fields. It should prove useful for rough estimations of genotypic variation in the vertical root distribution of upland rice because root growth angle is rapidly and easily measured.     

Comparison of QTLs for rice seedling morphology under different water supply conditions

The variation of seedling characteristics under different water supply conditions is strongly associated with drought resistance in rice (Oryza sativa L.) and a better elucidation of its genetics is helpful for improving rice drought resistance. Ninety-six doubled-haploid (DH)rice lines of an indica and japonica cross were grown in both flooding and upland conditions and QTLs for morphological traits at seedling stage were examined using 208 restriction fragment length polymorphism (RFLP) and 76 microsatellite (SSR) markers. A total of 32 putative QTLs were associated with the four seedling traits: average of three adventitious root lengths (ARL), shoot height (SH), shoot biomass (SW), and root to shoot dry weight ratio (RSR). Five QTLs detected were the same under control and upland conditions. The ratio between the mean value of the seedling trait under upland and flooding conditions was used for assessing drought tolerance. A total of six QTLs for drought tolerance were detected. Comparative analysis was performed for the QTLs detected in this case and those reported from two other populations with the same upland rice variety Azucena as parent. Several identical QTLs for seedling elongation across the three populations with the positive alleles from the upland rice Azucena were detected, which suggests that the alleles of Azucena might be involved in water stress-accelerated elongation of rice under different genetic backgrounds. Five cell wall-related candidate genes for OsEXP1, OsEXP2, OsEXP4, EXT, and EGase were mapped on the intervals carrying the QTLs for seedling traits.     

以回交重组自交系定位水稻萌芽期耐镉胁迫相关QTLs

水稻是世界上最主要的粮食作物之一,目前农用耕地存在土壤重金属污染的问题,而水稻对镉（Cd）等重金属的耐受性较低,进而使水稻产量和质量受到影响。定位稻种耐Cd胁迫相关数量性状基因座(quantitative trait loci, QTLs),对于指导水稻耐Cd育种具有重要意义。为发掘Cd胁迫相关基因,以粳稻02428和籼稻昌恢891衍生的124个回交重组自交系群体（backcross recombinant inbred ines,BILs）为材料,对水稻萌芽期的根长、芽长进行了分析,并对萌芽期与Cd胁迫相关的QTLs进行了定位分析。结果显示：Cd胁迫处理下,02428和昌恢891根长和芽长均受到显著抑制（P＜0.01）,其中Cd对根长的抑制强于芽长;QTL分析共检测到5个萌芽期与Cd胁迫相关的QTLs：qCdBL3、qCdRL7、qCdBL8.1、qCdBL8.2和qCdBL9分别位于水稻第3、7、8、8和9号染色体上,贡献率为6.45%~19.46%。其中,qCdBL3、qCdBL8.1、qCdBL8.2和qCdBL9与芽长相关,qCdRL7与根长相关。同时,检测到2个在对照条件下（水溶液）影响根长和芽长的QTLs：qCKBL8、qCKRL4,分别位于第8和4号染色体上,贡献率为10.53%和10.89%。比较显示,对照和Cd处理条件下控制水稻萌芽期根长或芽长的QTLs均不相同,说明Cd胁迫条件下,控制水稻根长和芽长的遗传机制可能不同于非Cd胁迫条件。研究结果为耐Cd基因的克隆和耐Cd水稻新品种的选育提供了参考。     

QTLs and Candidate Genes for Rice Root Growth Under Flooding and Upland Conditions

To investigate the genetic factors underlying constitutive and adaptive root growth under different water-supply conditions, a double haploid (DH) population, derived from a cross between lowland rice variety IR64 and upland rice variety Azucena, with 284 molecular markers was used in cylindrical pot experiments. Several QTLs for seminal root length (SRL), adventitious root number (ARN) and total root dry weight (RW) respectively, under both flooding and upland conditions were detected. Two identical QTLs for SRL and RW were found under flooding and upland conditions. The relative parameters defined as the ratio of parameters under the two water-supply conditions were also used for QTL analysis. A comparative analysis among different genetic populations was performed for the QTLs for root traits and several consistent QTLs for root traits across genetic backgrounds were detected. Candidate genes for cell expansion and elongation were used for comparative mapping with the detected QTLs. Four cell wall-related expressed sequence tags (ESTs) for OsEXP2, OsEXP4, EXT and Xet were mapped on the intervals carrying the QTLs for root traits.     

Identification of QTLs for Drought-Related Traits in Alien Introgression Lines Derived from Crosses of Rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> cv. IR64) × <Emphasis Type="Italic">O. glaberrima</Emphasis> under Lowland Moisture Stress

Drought is a major abiotic stress that limits rice productivity in rain-fed and upland ecosystems. African rice, Oryza glaberrima, has low yields but is tolerant to drought and other stresses. We evaluated 513 BC₂F₃ progenies from alien introgression lines (AILs) that were derived from crosses of Oryza sativa (IR64) × O. glaberrima. They were assessed for yield and other traits when grown under drought at two locations. Such conditions reduced grain production by 59% compared with the recurrent parent (IR64). However, 33 AILs had higher yields, thus demonstrating their potential as genetic material for transferring drought-related traits from O. glaberrima to O. sativa. A set of 200 AILs was selectively genotyped with 173 simple sequence repeat and sequenced tagged site markers. Molecular analysis showed that a mean of 4.5% of the O. glaberrima genome was introgressed in BC₂F₃ AILs. Our analysis revealed 33 quantitative trait loci (QTLs; including 10 novel) for different traits. O. glaberrima contributed 50% of the alleles to those newly identified QTLs, with one for grain yield per plant (ypp9.1) being new. A QTL at RM208 on chromosome 2 positively affected yield under stress, accounting for 22% of the genetic variation. Our identification of drought-related QTLs for yield and yield components will be useful to future research efforts in marker-assisted selection.     

淹水和干旱条件下水稻根系形成的QTLs及候选基因分析

为了研究不同水分条件下组成型根系性状和适应性根系性状的遗传机制,利用由IR64／Azucena发展的双单倍体（DH）群体分析了淹水和干旱条件下水稻幼苗种子根长（SRL）、不定根数（ARN）、总根干重（RW）及其对应的相对参数（干旱和淹水条件下根系性状的比值）的QTLs。淹水与干旱条件下检测到一个共同的种子根长QTL和一个共同的总根干重QTL。同时对前人发表的遗传群体定位的根系性状QTLs进行比较分析,检测到几个共同的根系性状QTLs。对与细胞伸长、分裂相关的候选基因进行了定位,其中4个细胞壁相关的ESTs（OsEXP2,OsEXP4,EXT和Xet）被定位在与不同水分条件下检测出的根系性状QTLs的相同区间。     

Whole plant responses, key processes, and adaptation to drought stress: the case of rice

Most high-yielding rice cultivars developed for irrigated conditions, including the widely grown lowland variety IR64, are highly susceptible to drought stress. This limits their adoption in rainfed rice environments where there is a risk of water shortage during the growing season. Mapping studies using lowland-by-upland rice populations have provided limited information about the genetic basis of variation in yield under drought. One approach to simultaneously improve and understand rice drought tolerance is to generate backcross populations, select superior lines in managed stress environments, and then evaluate which features of the selected lines differ from the recurrent parent. This approach was been taken with IR64, using a range of tolerant and susceptible cultivars as donor parents. Yields of the selected lines measured across 13 widely contracting water environments were generally greater than IR64, but genotype-by-environment effects were large. Traits expected to vary between IR64 and selected lines are plant height, because many donors were not semi-dwarf types, and maturity, because selection in a terminal stress environment is expected to favour earliness. In these experiments it was found that some lines that performed better under upland drought were indeed taller than IR64, but that shorter lines with good yield under drought could also be identified. In trials where drought stress developed in previously flooded (lowland) fields, height was not associated with performance. There was little change in maturity with selection. Other notable differences between IR64 and the selected backcross lines were in their responses to applied ABA and ethylene in greenhouse experiments at the vegetative stage and in leaf rolling observed under chronic upland stress in the field. These observations are consistent with the hypothesis that adaptive responses to drought can effectively allow for improved performance across a broad range of water environments. The results indicate that the yield of IR64 under drought can be significantly improved by backcrossing with selection under stress. In target environments where drought is infrequent but significant in certain years, improved IR64 with greater drought tolerance would be a valuable option for farmers.     

Analysis of QTLs for yield-related traits in Yuanjiang common wild rice （Oryza rufipogon Griff.）

Using an accession of common wild rice(Oryza rufipogon Griff.)collected from Yunnjiang County,Yunnan Province,China,as the donor and an elite cnltivar 93-11,widely used in two-line indica hybrid rice production in China,as the recurrent parent,an advanced backcross populations were developed.Through genotyping of 187 SSR markers and investigation of six yield-related traits of two generations(BC4F2 and BC4F4),a total of 26 QTLs were detected by employing single point analysis and interval mapping in both generations.Of the 26 QTLs,the alleles of 10(38.5%)QTLs originating from O.rufipogon had shown a beneficial effect for yield-related traits in the 93-11 genetic background.In addition,five QTLs controlling yield and its components were newly identified,indicating that there arc potentially novel alleles in Yuanjiang common wild rice.Three regions underling significant QTLs for several yield-related traits were detected on chromosome 1,7 and 12.The QTL clusters were founded and corresponding agronomic traits of those QTLs showed highly significant correlation,suggesting the pleiotropism or tight linkage.Fine-mapping and cloning of these yield-related QTLs from wild rice would be helpful to elucidating molecular mechanism of rice domestication and rice breeding in the future.     

Analysis of QTLs for yield-related traits in Yuanjiang common wild rice (Oryza rufipogon Griff.)

Using an accession of common wild rice (Oryza rufipogon Griff.) collected from Yuanjiang County, Yunnan Province, China, as the donor and an elite cultivar 93-11, widely used in two-line indica hybrid rice production in China, as the recurrent parent, an advanced backcross populations were developed. Through genotyping of 187 SSR markers and investigation of six yield-related traits of two gen- erations (BC4F2 and BC4F4), a total of 26 QTLs were detected by employing single point analysis and inte...     

Identification of QTLs associated with agronomic performance under nitrogen-deficient conditions using chromosome segment substitution lines of a wild rice relative, <Emphasis Type="Italic">Oryza rufipogon</Emphasis>

Improved root system architecture can enhance agronomic performance by increasing water and nitrogen (N) acquisition efficiency. However, little is known about interaction between root system architecture and agronomic performance under field environments. To gain a better understanding about the genetic basis of these relationships, we evaluated a set of chromosome segment substitution lines (CSSLs) derived from crosses between a tropical japonica rice cultivar ‘Curinga’ and a wild species Oryza rufipogon accession IRGC105491. Root system architectural traits were investigated using the CSSLs at 40 days old seedlings using the root basket method under hydroponic conditions, and agronomic performances were also tested under field conditions with different N treatments. Agronomic performances were computed as the ratio of a trait value under low to high N treatments, including grain yield and biomass yield as nitrogen-deficiency tolerance (NDT) traits. Root architecture and NDT trait QTLs were mapped using 238 SNP marker loci. A total of 13 QTLs for root system architectural, NDT and morpho-physiological traits were identified on chromosomes 1, 3, 4, 5, 7, 8, 9, 10 and 12. Interestingly, a QTL for deeper root number was identified the region of SNP markers between id1012330 and id1021697 on chromosome 1 under hydroponic conditions overlapped with a QTL for NDT trait of relative grain yield (qRGY1). These results suggest that deeper root trait is helpful to maintain grain yield under nitrogen-deficient conditions. The QTL associated root architecture could potentially be used in future rice-breeding efforts to increase agronomic performance under nitrogen-deficient conditions.     

Quantitative trait loci for root-penetration ability and root thickness in rice: comparison of genetic backgrounds.

Drought is the major abiotic stress limiting rice (Oryza sativa) production and yield stability in rainfed lowland and upland ecosystems. Root systems play an important role in drought resistance. Incorporation of root selection criteria in drought resistance improvement is difficult due to lack of reliable and efficient screening techniques. Using a wax-petrolatum layer system simulated to compacted soil layers, root traits were evaluated in a doubled haploid (DH) population derived from the cross between 'IR64' and 'Azucena'. Twelve putative QTLs (quantitative trait loci) were detected by interval mapping comprising four QTLs for root-penetration ability, four QTLs for root thickness, two QTLs for penetrated root number, and two QTLs for total root number. These QTLs individually explained 8.4% to 16.4% of the phenotypic variation. No QTL was detected for maximum penetrated root length by interval mapping. One QTL located between RG104 and RG348 was found to influence both root-penetration ability and root thickness. QTLs for root-penetration ability and root thickness were compared across two populations, 'IR64'-'Azucena' and 'CO39'-'Moroberekan', and different testing conditions. The identified consistent QTLs could be used for marker-assisted selection for deep and thick roots with high root-penetration ability in rice.     

Evaluating the resistance of six rice cultivars to drought: restriction of deep rooting and the use of raised beds

Soil water deficits reduce rice (Oryza sativa L.) productivity under upland field conditions. In this study, we constructed screening facilities to evaluate the performance of rice cultivars under drought conditions and to assess the roles of deep roots. Two experiments were conducted with six rice cultivars, including drought-tolerant and drought-susceptible cultivars, grown in two root environments: a root-restricted treatment that restricted rooting depth with water-permeable sheets, and a raised bed that reduced water availability in the surface soil by inserting a gravel layer between the topsoil and subsoil layers to interrupt capillary transport of water. In the root-restricted treatment, in which root growth was restricted to the surface 25-cm layer, leaf water potential decreased faster in cultivars with a large canopy during drought stress, and there was little difference in panicle weight among cultivars. With a normal (unrestricted) root environment, the deepest-rooting cultivar (‘IRAT109’) maintained higher leaf water potential during drought, although panicle weight under drought stress was affected by yield potential as well as by deep rooting. Under the intermittent drought stress in the raised bed, deep-rooting cultivars accumulated more nitrogen and produced more biomass, and the difference in panicle weight between deep-rooting drought-tolerant and shallow-rooting drought-susceptible cultivars was magnified by the raised bed compared with the yield differences under drought in a normal root environment. These results demonstrate that the drought screening facilities we developed can help to identify superior cultivars under upland field conditions without time-consuming measurement of deep root systems.     

Meta-analysis of quantitative trait loci for grain yield and component traits under reproductive-stage drought stress in an upland rice population

A recombinant inbred population developed from a cross between high-yielding lowland rice (Oryza sativa L.) subspecies indica cv. IR64 and upland tropical rice subspecies japonica cv. Cabacu was used to identify quantitative trait loci (QTLs) for grain yield (GY) and component traits under reproductive-stage drought stress. One hundred fifty-four lines were grown in field trials in Indonesia under aerobic conditions by giving surface irrigation to field capacity every 4 days. Water stress was imposed for a period of 15 days during pre-flowering by withholding irrigation at 65 days after seeding. Leaf rolling was scored at the end of the stress period and eight agronomic traits were evaluated after recovery. The population was also evaluated for root pulling force, and a total of 201 single nucleotide polymorphism markers were used to construct the molecular genetic linkage map and QTL mapping. A QTL for GY under drought stress was identified in a region close to the sd1 locus on chromosome 1. QTL meta-analysis across diverse populations showed that this QTL was conserved across genetic backgrounds and co-localized with QTLs for leaf rolling and osmotic adjustment (OA). A QTL for percent seed set and grains per panicle under drought stress was identified on chromosome 8 in the same region as a QTL for OA previously identified in three different populations.