Comparison of phenotypic versus marker-assisted background selection for the SUB1 QTL during backcrossing in rice

Marker assisted backcrossing has been used effectively to transfer the submergence tolerance gene SUB1 into popular rice varieties, but the approach can be costly. The selection strategy comprising foreground marker and phenotypic selection was investigated as an alternative. The non-significant correlation coefficients between ranking of phenotypic selection and ranking of background marker selection in BC₂F₁, BC₃F₁ and BC₃F₂ generations indicated inefficiency of phenotypic selection compared to marker-assisted background selection with respect to recovery of the recipient genome. In addition, the introgression size of the chromosome fragment containing SUB1 was approximately 17 Mb, showing the effects of linkage drag. The significant correlation coefficient between rankings of phenotypic selection with the percentage of recipient alleles in the BC₁F₁ generation suggested that background selection could be avoided in this generation to minimize the genotyping cost. The phenotypically selected best plant of the BC₃F₁ generation was selfed and backcross recombinant lines were selected in the resulting BC₃F₄ generation. The selection strategy could be appropriate for the introgression of SUB1 QTL in countries that lack access to high-throughput genotyping facilities.     

Variation in heading date conceals quantitative trait loci for other traits of importance in breeding selection of rice

To identify quantitative trait loci (QTLs) associated with the primary target traits for selection in practical rice breeding programs, backcross inbred lines (BILs) derived from crosses between temperate japonica rice cultivars Nipponbare and Koshihikari were evaluated for 50 agronomic traits at six experimental fields located throughout Japan. Thirty-three of the 50 traits were significantly correlated with heading date. Using a linkage map including 647 single-nucleotide polymorphisms (SNPs), a total of 122 QTLs for 38 traits were mapped on all rice chromosomes except chromosomes 5 and 9. Fifty-eight of the 122 QTLs were detected near the heading date QTLs Hd16 and Hd17 and the remaining 64 QTLs were found in other chromosome regions. QTL analysis of 51 BILs having homozygous for the Koshihikari chromosome segments around Hd16 and Hd17 allowed us to detect 40 QTLs associated with 27 traits; 23 of these QTLs had not been detected in the original analysis. Among the 97 QTLs for the 30 traits measured in multiple environments, the genotype-by-environment interaction was significant for 44 QTLs and not significant for 53 QTLs. These results led us to propose a new selection strategy to improve agronomic performance in temperate japonica rice cultivars.     

Confirming a major QTL and finding additional loci responsible for field resistance to brown spot (Bipolaris oryzae) in rice

Brown spot is a devastating rice disease. Quantitative resistance has been observed in local varieties (e.g., ‘Tadukan’), but no economically useful resistant variety has been bred. Using quantitative trait locus (QTL) analysis of recombinant inbred lines (RILs) from ‘Tadukan’ (resistant) × ‘Hinohikari’ (susceptible), we previously found three QTLs (qBS2, qBS9, and qBS11) that conferred resistance in seedlings in a greenhouse. To confirm their effect, the parents and later generations of RILs were transplanted into paddy fields where brown spot severely occurred. Three new resistance QTLs (qBSfR1, qBSfR4, and qBSfR11) were detected on chromosomes 1, 4, and 11, respectively. The ‘Tadukan’ alleles at qBSfR1 and qBSfR11 and the ‘Hinohikari’ allele at qBSfR4 increased resistance. The major QTL qBSfR11 coincided with qBS11 from the previous study, whereas qBSfR1 and qBSfR4 were new but neither qBS2 nor qBS9 were detected. To verify the qBSfR1 and qBSfR11 ‘Tadukan’ resistance alleles, near-isogenic lines (NILs) with one or both QTLs in a susceptible background (‘Koshihikari’) were evaluated under field conditions. NILs with qBSfR11 acquired significant field resistance; those with qBSfR1 did not. This confirms the effectiveness of qBSfR11. Genetic markers flanking qBSfR11 will be powerful tools for marker-assisted selection to improve brown spot resistance.     

Variation in cooking and eating quality traits in Japanese rice germplasm accessions

The eating quality of cooked rice is important and determines its market price and consumer acceptance. To comprehensively describe the variation of eating quality in 183 rice germplasm accessions, we evaluated 33 eating-quality traits including amylose and protein contents, pasting properties of rice flour, and texture of cooked rice grains. All eating-quality traits varied widely in the germplasm accessions. Principal-components analysis (PCA) revealed that allelic differences in the Wx gene explained the largest proportion of phenotypic variation of the eating-quality traits. In 146 accessions of non-glutinous temperate japonica rice, PCA revealed that protein content and surface texture of the cooked rice grains significantly explained phenotypic variations of the eating-quality traits. An allelic difference based on simple sequence repeats, which was located near a quantitative trait locus (QTL) on the short arm of chromosome 3, was associated with differences in the eating quality of non-glutinous temperate japonica rice. These results suggest that eating quality is controlled by genetic factors, including the Wx gene and the QTL on chromosome 3, in Japanese rice accessions. These genetic factors have been consciously selected for eating quality during rice breeding programs in Japan.     

Cytoplasm and cytoplasm-nucleus interactions affect agronomic traits in japonica rice

Some sources of cytoplasm have been favoredin rice breeding for unknown reasons. Tostudy cytoplasmic effects on agronomictraits, five core japonica parents inOryza sativa, Xinan 175, Reimei,Keqing No. 3, Todorokiwase, and Toride No.1, which are ancestors of 75 % of cultivarsbred in Yunnan, China, were used as femaleparents in crosses with 3 distinctjaponica rice cultivars, 8-126,Lijiangxintuanheigu, and Norinmochi No.20as males. These nuclear genomes weresubstituted into the five cytoplasms viaseven backcrosses using the original maleas recurrent parent. Fifteen combinationsof BC₇F₂ and their parents weresown in Jinghong during the late season(July-October) for agronomic evaluation in1999. Meanwhile, all materials werescreened for low temperature tolerancebased upon two methods in Kunming (1916 mabove sea level): natural field and lowtemperature water (19 °C) cyclingirrigation at booting stage. Spikeletfertility was used as an indication of lowtemperature tolerance. Effects of cytoplasmon yield, width of flag leaf, and lowtemperature tolerance were significant. Significant cytoplasm-nucleus interactionon yield, plant height, and low temperaturetolerance were also observed. These resultsindicated that cytoplasm andcytoplasm-nucleus interaction playedimportant roles in yield, low temperaturetolerance, and some important agronomictraits in japonica rice. The role ofcytoplasm and cytoplasm-nucleus interactionshould be considered in future ricebreeding and resources work.     

水稻灌浆期叶片蛋白质差异表达及其作用机理分析

采用双向电泳和质谱技术研究大穗型水稻“金恢809”灌浆期旗叶的蛋白质表达模式,共发现17个蛋白质发生差异表达,其中3个在灌浆前期至中期大量表达,9个在中后期大量表达,4个在后期大量表达,1个在灌浆前期和后期出现两次表达高峰。经MALDI-TOF/MS分析和数据库检索,鉴定出12个差异蛋白质,分别参与叶片的物质合成与降解,碳水化合物运输,植株抗氧化反应,激素代谢,以及细胞骨架的构建和组织成熟等生理反应。分析结果表明,核糖/半乳糖/甲基半乳糖苷运输ATP结合蛋白1在灌浆前中期参与物质向籽粒的运输;生长素响应蛋白IAA27通过调节ATPase活性影响叶片物质运输;N-乙酰谷氨酸半醛脱氢酶在灌浆末期参与叶片的多胺代谢,延缓叶片衰老;谷胱甘肽S-转移酶和Cu/Zn-超氧化物歧化酶在籽粒灌浆后期的植物解毒和防御活性氧伤害中起着重要作用。     

两个水稻品种镉积累相关基因表达及其分子调控机制

内源小干扰RNAs (small interfering RNAs, siRNAs)和DNA甲基化在植物生长发育和适应环境胁迫中调控基因的表达。对于植物来说, 镉(Cadmium, Cd)是一种非必需且具有毒性的元素。为研究DNA甲基化和siRNAs在水稻(Oryza sativa L.) Cd积累相关基因表达调控方面的作用, 比较了Cd高积累品种(秀水110)和Cd低积累品种(秀水11)中Cd积累相关基因的表达情况。结果表明, 在秀水110和秀水11叶片中, 除植物Cd抗性蛋白(plant cadmium resistance protein, PCR)基因家族成员OsPCR1的表达水平呈现出显著的差异外, 其他Cd积累相关基因的表达水平不存在显著的差异。说明OsPCR1基因可能参与调控水稻体内Cd的积累。利用荧光实时定量PCR (qRT-PCR)技术研究了水稻叶片中siRNA表达水平在水稻5个不同生长发育期中的变化情况。数据显示水稻叶片中与OsPCR1基因外显子2匹配的siRNA的丰度和OsPCR1基因的表达水平呈负相关。进一步利用McrBC-qRT-PCR技术研究OsPCR1基因外显子2甲基化水平在水稻5个不同生长发育期中的变化情况表明, 在Cd处理条件下水稻叶片中OsPCR1基因外显子2甲基化水平和该基因的表达水平也呈负相关。说明, 在水稻体内Cd积累的过程中, 该siRNA和OsPCR1基因外显子2甲基化可能参与调控OsPCR1基因的表达。这些结果对于研究OsPCR1基因的功能和培育Cd低积累水稻品种具有重要的理论指导意义。     

水稻黑条矮缩病抗性评价方法及抗性资源筛选

水稻黑条矮缩病是水稻主要病毒病害之一。目前由于缺乏规模、高效的黑条矮缩病抗性鉴定体系,制约了抗黑条矮缩病水稻资源的发掘,限制了抗黑条矮缩病的育种进程和基础研究。本研究通过分析水稻黑条矮缩病田间鉴定所需灰飞虱的有效接种密度、带毒率及播期等,提出水稻黑条矮缩病田间鉴定有效接种的灰飞虱密度在800万头 hm^-2左右较为合理,而带毒率应不低于5%。并进一步对现有黑条矮缩病人工接种鉴定的循回期、接种虫量、接种时间及虫龄等进行了优化。利用上述鉴定体系,2010年对来源于20个国家的共1240份水稻种质进行黑条矮缩病田间鉴定,初步获得发病率低于10%的品种34个;2011、2012连续两年对该34个品种进行多年多点重复抗性鉴定,发现来自东南亚地区的3个品种Kanyakumari 29、Madurai 25和Vietnam 160连续3年发病率均低于10%,表现较高的黑条矮缩病的抗性。进一步分期播种鉴定的结果表明,Kanyakumari29在3个播期、3个鉴定点的发病率均低于12%,而Madurai 25和Vietnam 160发病率均低于9%。此外,在人工接种条件下Kanyakumari 29、Madurai 25和Vietnam 160的发病率均低于9%。因此,多年多点田间鉴定和人工室内接种鉴定的结果均表明,Kanyakumari 29、Madurai 25和Vietnam 160稳定、高抗黑条矮缩病。综上所述,本研究建立的田间鉴定与室内鉴定相结合的黑条矮缩病鉴定体系准确、可靠,可用于黑条矮缩病的大规模鉴定,该体系的建立及高抗黑条矮缩病水稻资源的发掘为水稻抗黑条矮缩病基因的鉴定及育种利用提供了重要的方法和材料基础。     

Mapping and validation of QTLs for rice sheath blight resistance

Sheath blight, caused by Rhizoctonia solani, is one of the most serious diseases of rice. Among 33 rice accessions, mainly from National Institute of Agrobiological Sciences (NIAS) Core Collection, we found three landraces from the Himalayas—Jarjan, Nepal 555 and Nepal 8—with resistance to sheath blight in 3 years’ field testing. Backcrossed inbred lines (BILs) derived from a cross between Jarjan and the leading Japanese cultivar Koshihikari were used in QTL analyses. Since later-heading lines show fewer lesions, we used only earlier-heading BILs to avoid association with heading date. We detected eight QTLs; the Jarjan allele of three of these increased resistance. Only one QTL, on chromosome 9 (between markers Nag08KK18184 and Nag08KK18871), was detected in all 3 years. Chromosome segment substitution lines (CSSLs) carrying it showed resistance in field tests. Thirty F₂ lines derived from a cross between Koshihikari and one CSSL supported the QTL.     

Quantitative trait loci for whiteness of cooked rice detected in improved rice cultivars in Hokkaido

Improving the eating quality of cooked rice has been one of the most important objectives in rice breeding programs. Eating quality of cooked rice is a complex trait including several components, such as external appearance, taste, aroma, and texture. Therefore, dissection of these components followed by marker-assisted selection of detected QTL(s) may be a useful approach for achieving desirable eating quality in rice breeding. Whiteness of cooked rice (WCR) is an important factor related to the external appearance of cooked rice. WCR is known to be associated with the amylose and protein contents of the endosperm. However, the genetic basis of WCR remains unclear. In this study, we evaluated phenotypic variation in WCR among recently developed rice cultivars from Hokkaido, Japan. Then, we developed doubled haploid lines (DHLs) derived from a cross between two cultivars from Hokkaido, Joiku No. 462 (high WCR) and Jokei06214 (low WCR). Using the DHLs, we detected two QTLs for WCR, qWCR3 and qWCR11, on chromosomes 3 and 11, respectively. We also examined the dosage effect of the two QTLs based on both the categorized segregants in the DHLs and the relationship between the WCR phenotype and inheritance around the QTL regions in cultivars from Hokkaido.     

利用分子标记辅助选择将抗稻瘟病基因Pi-9(t)渗入水稻恢复系泸恢17

本研究采用杂交和分子标记辅助选择技术,将亲本材料P2的水稻广谱高抗稻瘟病基因Pi-9(t)导入杂交水稻恢复系泸恢17,再利用抗稻瘟病基因Pi-9(t)的特异分子标记pB8检测该目的基因,获得68份携有Pi-9(t)基因型的回交株系。基因型鉴定表明株系WR1023、WR1043、WR1056和WR1062为均含有Pi-9(t)基因纯合的回交后代株系。表型分析表明WR1023和WR1056株系农业性状已稳定,且其株叶型、抗稻瘟病及配合力较好,我们认为可以用作育种抗性亲本材料。     

QTL analysis for panicle characteristics in temperate japonica rice

To understand the genetic background of panicle characteristics in temperate japonica rice (Oryza sativa L.), we genetically analyzed DH lines derived from a cross between two temperate japonica rice cultivars, ‘Akihikari’ and ‘Koshihikari’,in 1996 and 1997. Four traits of panicle characteristics, number of primary branches per panicle (NPB), number of secondary branches per panicle (NSB), average number of spikelets on one primary branch (NSP)and average number of spikelets on one secondary branch (NSS), in 212 DH lines were measured, and the interval mapping of QTLs for these traits was carried out using169 DNA markers with an LOD threshold of2.5. Five, three and one putative QTLs for NPB, NSB and NSS were identified,respectively, and no QTLs relating to NSP appeared. The percentages in total phenotypic variation explained by all putative QTLs for NPB were 35.5%: and43.8% in 1996 and 1997, respectively. All putative QTLs for NSB accounted for 35.5%and 27.5% of total phenotypic variation in1996 and 1997, respectively. The QTLs identified in this study will be useful intemperate japonica rice breeding for improved spikelet yield. This revised version was published online in August 2006 with corrections to the Cover Date.     

Characterization and fine mapping of thermo-sensitive chlorophyll deficit mutant1 in rice (Oryza sativa L.)

Chlorophyll content is one of the most important traits controlling crop biomass and economic yield in rice. Here, we isolated a spontaneous rice mutant named thermo-sensitive chlorophyll deficit 1 (tscd1) derived from a backcross recombinant inbred line population. tscd1 plants grown normally from the seedling to tiller stages showed yellow leaves with reduced chlorophyll content, but showed no significant differences after the booting stage. At temperatures below 22°C, the tscd1 mutant showed the most obvious yellowish phenotype. With increasing temperature, the yellowish leaves gradually turned green and approached a normal wild type color. Wild type and tscd1 mutant plants had obviously different chloroplast structures and photosynthetic pigment precursor contents, which resulted in underdevelopment of chloroplasts and a yellowish phenotype in tscd1. Genetic analysis indicated that the mutant character was controlled by a recessive nuclear gene. Through map-based cloning, we located the tscd1 gene in a 34.95 kb region on the long arm of chromosome 2, containing two BAC clones and eight predicted candidate genes. Further characterization of the tscd1 gene is underway. Because it has a chlorophyll deficit phenotype before the tiller stage and little influence on growth vigor, it may play a role in ensuring the purity of hybrids.     

Genetic variation in resistance to blast disease (Pyricularia oryzae Cavara) in Japanese rice (Oryza sativa L.), as determined using a differential system

A total of 324 Japanese rice accessions, including landrace, improved, and weedy types were used to 1) investigate genetic variations in blast resistance to standard differential isolates, and 2) across the genome using polymorphism data on 64 SSR markers. From the polymorphism data, the accessions were classified into two clusters. Accessions from irrigated lowland areas were included mainly in cluster I, and upland and Indica types were mainly in cluster II. The accessions were classified into three resistance subgroups, A2, B1 and B2, based on the reaction patterns to blast isolates. The accessions in A2 were postulated to have at least two resistance genes Pish and Pik-s, whereas those in B1 had various combinations of the resistance genes Pish, Pia, Pii, Pi3, Pi5(t), and Pik alleles. The B2 accessions were resistant to almost all isolates, and many accessions of cluster II were included, and had Pish, Pia, Pii, Pi3, Pi5(t), certain Pik, Piz and Pita alleles, and unknown genes. The frequencies of accessions of B1 originating in Hokkaido, and those of B2 originating in the Kanto and Tohoku regions were remarkably higher than in the other regions.     

Genome-wide association mapping focusing on a rice population derived from rice breeding programs in a region

Plant breeding programs in local regions may generate genetic variations that are desirable to local populations and shape adaptability during the establishment of local populations. To elucidate genetic bases for this process, we proposed a new approach for identifying the genetic bases for the traits improved during rice breeding programs; association mapping focusing on a local population. In the present study, we performed association mapping focusing on a local rice population, consisting of 63 varieties, in Hokkaido, the northernmost region of Japan and one of the northern limits of rice cultivation worldwide. Six and seventeen QTLs were identified for heading date and low temperature germinability, respectively. Of these, 13 were novel QTLs in this population and 10 corresponded to the QTLs previously reported based on QTL mapping. The identification of QTLs for traits in local populations including elite varieties may lead to a better understanding of the genetic bases of elite traits. This is of direct relevance for plant breeding programs in local regions.     

Genetical and morphological characterization of cold tolerance at fertilization stage in rice

Cold temperature during the reproductive phase leads to seed sterility, which reduces yield and decreases the grain quality of rice. The fertilization stage, ranging from pollen maturation to the completion of fertilization, is sensitive to unsuitable temperature. Improving cold tolerance at the fertilization stage (CTF) is an important objective of rice breeding program in cold temperature areas. In this study, we characterized fertilization behavior under cold temperature to define the phenotype of CTF and identified quantitative trait loci (QTLs) for CTF. A wide variation in CTF levels has been identified among local cultivars in Hokkaido, which is one of the most northern regions for rice cultivation in the world. Clear varietal differences in pollen germination, and pollen tube elongation due to cold temperature have been observed. These differences may confer a degree of CTF among this population. We conducted QTL analysis for CTF using 120 backcrossed inbred lines derived from a cross between Eikei88223 (vigorous CTF) and Suisei (very weak CTF). Three QTLs for CTF were identified. A clear effect by QTL, qCTF7, for increasing the level of CTF was validated using advanced progeny. These results will facilitate marker-assist selection for desirable QTLs for CTF in rice breeding program.     

Inheritance of resistance to rice stripe virus in rice line `BL 1'

Rice stripe is the most serious virus disease in temperate rice-growing countries. The most economical and environmentally safe practice for controlling this disease is virus-resistant cultivars. ‘BL 1’ is an elite germplasm line with the blast resistance gene Pib, and has been used as a differential line for testing the pathogenicity of the blast fungus. We found that certain progenies from BL 1 showed resistance to both blast and rice stripe virus (RSV). The objectives of this study were to evaluate the RSV resistance in the field and under artificial conditions, to assess the reaction to the insect vector(small brown plant hopper, SBPH), and to examine its inheritance and its relationship to blast resistance in BL 1.BL 1 was susceptible to SBPH, but resistant to RSV in field and artificial inoculation tests. The inheritance of RSV resistance in F₃ lines from the cross Nipponbare (NPB)/BL 1 was studied using artificial inoculation with a population of viruliferous SBPH. A serological assay for RSV infection using an enzyme-linked immunosorbent assay (ELISA) was used. RSV resistance in BL 1 was controlled by a single major gene with incomplete dominance. The locus responsible for RSV resistance was genetically independent of the blast resistance gene Pib. The resistance gene for RSV infection in BL 1 was also independent of Stvb-i, a gene widely distributed in resistant Japanese cultivars. Resistance to RSV must be diversified in rice cultivars considering the potential for future emergence of new RSV strains. The new resistance gene identified in BL 1, which has improved plant type and blast resistance, is considered useful for breeding RSV-resistant cultivars in japonica rice. This revised version was published online in August 2006 with corrections to the Cover Date.     

北方粳稻产量与品质性状及其相互关系分析

随着稻作科学研究的发展和人民生活水平的提高,我国对粳稻需求持续增加,粳稻面积不断扩大,明确目前不同稻区产量与品质性状现状及其相互关系,对今后北方粳稻育种有重要参考价值。本文利用2011—2013年北方稻区国家水稻新品种试验数据,根据地区和品种(系)特点划分为黄淮粳稻、京津唐粳稻、晚熟中早粳稻、中熟中早粳稻、早熟中早粳稻5种类型,分析了产量水平、产量构成因素、品质现状等类型间差异及其相互关系。结果表明,产量表现为中熟中早粳稻早熟中早粳稻、京津唐粳稻、黄淮粳稻晚熟中早粳稻。5种类型糙米率和整精米率平均值分别为83.66%和66.95%,垩白粒率和垩白度平均值分别为30.26%和3.08%。总体和不同类型产量与糙米率、精米率和整精米率均表现为显著的正相关,结实率与糙米率、精米率和整精米率均表现为显著的正相关,与垩白粒率表现为显著的负相关。籽粒长宽比与产量关系不密切,与糙米率大多显著负相关,而与整精米率的负相关均未达到显著水平。着粒密度与产量的关系也不密切,与穗数基本表现为显著负相关而与每穗粒数均表现为显著正相关,对结实率、千粒重和主要品质性状影响不大。根据上述结果可以认为,我国北方粳稻至少在9 t hm–2以下产量与主要品质性状的矛盾并不突出,可以在保持产量的基础上改进品质,或者在保持品质的基础上提高产量,使产量和品质在更高水平上达成新的平衡。     

Genetic dissection of black grain rice by the development of a near isogenic line

Rice (Oryza sativa L.) can produce black grains as well as white. In black rice, the pericarp of the grain accumulates anthocyanin, which has antioxidant activity and is beneficial to human health. We developed a black rice introgression line in the genetic background of Oryza sativa L. ‘Koshihikari’, which is a leading variety in Japan. We used Oryza sativa L. ‘Hong Xie Nuo’ as the donor parent and backcrossed with ‘Koshihikari’ four times, resulting in a near isogenic line (NIL) for black grains. A whole genome survey of the introgression line using DNA markers suggested that three regions, on chromosomes 1, 3 and 4 are associated with black pigmentation. The locus on chromosome 3 has not been identified previously. A mapping analysis with 546 F₂ plants derived from a cross between the black rice NIL and ‘Koshihikari’ was evaluated. The results indicated that all three loci are essential for black pigmentation. We named these loci Kala1, Kala3 and Kala4. The black rice NIL was evaluated for eating quality and general agronomic traits. The eating quality was greatly superior to that of ‘Okunomurasaki’, an existing black rice variety. The isogenicity of the black rice NIL to ‘Koshihikari’ was very high.     

Identification of qRL7, a major quantitative trait locus associated with rice root length in hydroponic conditions

Root system development is an important target for improving yield in rice. Active roots that can take up nutrients more efficiently are essential for improving grain yield. In this study, we performed quantitative trait locus (QTL) analyses using 215 recombinant inbred lines derived from a cross between Xieqingzao B (XB), a maintainer line with short roots and R9308, a restorer line with long roots. Only a QTLs associated with root length were mapped on chromosomes 7. The QTL, named qRL7, was located between markers RM3859 and RM214 on chromosome 7 and explained 18.14–18.36% of the total phenotypic variance evaluated across two years. Fine mapping of qRL7 using eight BC₃F₃ recombinant lines mapped the QTL to between markers InDel11 and InDel17, which delimit a 657.35 kb interval in the reference cultivar Nipponbare. To determine the genotype classes for the target QTL in these BC₃F₃ recombinants, the root lengths of their BC₃F₄ progeny were investigated, and the result showed that qRL7 plays a crucial role in root length. The results of this study will increase our understanding of the genetic factors controlling root architecture, which will help rice breeders to breed varieties with deep, strong and vigorous root systems.