Characterization of near-isogenic lines carrying QTL for high spikelet number with the genetic background of an indica rice variety IR64 (Oryza sativa L.)

Total spikelet number per panicle (TSN) is one of the most important traits associated with rice yield potential. This trait was assessed in a set of 334 chromosomal segment introgression lines (ILs: BC₃-derived lines), developed from new plant type (NPT) varieties as donor parents and having the genetic background of an indica-type rice variety IR64. Among the 334 ILs, five lines which had different donor parents and showed significantly higher TSN than IR64 were used for genetic analysis. Quantitative trait locus (QTL) analysis was conducted using F₂ populations derived from crosses between IR64 and these ILs. As a result, a QTL for high TSN (one from each NPT donor variety) was detected on common region of the long arm of chromosome 4. The effect of the QTL was confirmed by an increase in TSN of five near-isogenic lines (NILs) developed in the present study. The variation in TSN was found among these NILs, attributing to the panicle architecture in the numbers of primary, secondary and tertiary branches. The NILs for TSN and the SSR markers linked to the TSN QTLs are expected to be useful materials for research and breeding to enhance the yield potential of rice varieties.     

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 new QTL for salt tolerance from rice variety Pokkali

Salt stress is an ever-present threat to rice production worldwide. Rice salinity tolerance is complex, both genetically and physiologically. The success and effectiveness in selecting salt-tolerant rice variety require the identification of QTL for the tolerance and closely linked molecular markers. In the present study, a RIL population consisting of 148 lines, derived from a cross between IR29 (salt-sensitive) and Pokkali (salt-tolerant), was used to identify new QTL for salt tolerance and investigate the relationships between salt stress caused injury and the changes in different physiological and morphological traits at the seedling stage. 14,470 high-quality SNP markers generated by the Rice 56K SNP array were converted to 1,467 bin markers for linkage mapping. A high-density genetic linkage map covering 1,680.9 cM was constructed, with the physical to genetic distance ratio being 222 Kb/cM. In total, 23 QTL for different salt tolerance indices were identified, including the previously reported Saltol which is currently used in breeding programmes. Three QTL for salt injury score (SIS) were located on chromosomes 1, 4 and 12, all being closely related to the long-distant Na⁺ transport from roots to shoots. These QTL showed additive effects, thus can be effectively used in breeding programme to pyramid various tolerance genes.     

籼稻背景下导入Wx~(in)等位基因改良稻米食味和理化品质

水稻Wx~b等位基因已广泛用于籼稻的品质改良,但携带该等位基因的一些籼稻米饭往往偏软,仍需进一步改良。为明确籼稻背景下导入Wxin等位基因对稻米食味品质和理化品质的效应,分别以携带Wxin的IR64和携带Wx~b的9311为供体,以携带Wxa的籼稻SIR3611 (3611)为受体,基于分子标记辅助选择,通过杂交和连续回交的方式构建了3611背景下携带Wxin和Wx~b的近等基因系。系统比较了不同近等基因系间的农艺性状以及稻米的食味和理化品质。结果表明,近等基因系与受体亲本3611的主要农艺性状基本接近,无显著差异。NIL(Wxin)稻米的表观直链淀粉含量较亲本3611极显著下降而胶稠度极显著增加。NIL(Wx~b)稻米表观直链淀粉含量最低且与之对应的胶稠度最高。近等基因系NIL(Wxin)和NIL(Wx~b)稻米的食味值较亲本极显著提高。NIL(Wx~(in))和NIL(Wx~b)稻米的GBSSI丰度与对应的表观直链淀粉含量具有明显的正相关。稻米粉的黏滞性谱、热糊化特性和晶体结构与直链淀粉含量显著相关性。本研究为在我国籼稻品种品质改良中有效利用Wxin等位基因提供了重要依据。     

应用导入系群体进行水稻产量相关性状的遗传剖析

以优质高产水稻品种丰矮占为轮回亲本, 以Khazar和IR64作供体亲本, 经连续回交分别构建了2套导入系(introgression lines)群体。对导入系后代分别在广州早造和晚造两种环境下进行重复产量鉴定。对两环境下产量及其组分性状的相关分析表明, 在广州早造和晚造环境下水稻产量构成因素存在很大差异。在早造, 每穗实粒数对产量供献最大, 而在晚造, 单株有效穗数对产量供献最大。应用SSR分子标记对这些导入系的供体片段进行全基因组扫描并应用单向方差分析(one-way ANOVA)剖析了导入系基因型与其产量及其组分的关系, 共检测到27个染色体区段与产量及组分性状相关, 包括10个产量QTL、9个单株穗数QTL、9个每穗实粒数QTL和14个千粒重QTL。大多数QTL只在一个环境条件下表达。在第3、7和9染色体上有3个QTL区域与产量及其两个组分有较大的效应, 值得关注。最终, 本研究在同步进行复杂农艺性状的改良和遗传剖析的研究上做出了有益的尝试。     

Breeding and characterization of the world’s first practical rice variety with resistance to brown spot (Bipolaris oryzae) bred using marker-assisted selection

Brown spot (BS) caused by Bipolaris oryzae is a serious disease of rice and decreases grain yield. Breeding for BS resistance is an economical solution but has not hitherto been achieved. To develop a practical BS-resistant variety, we introduced a chromosomal segment including a quantitative trait locus (QTL) for BS resistance, qBSfR11, derived from the BS-resistant local resource ‘Tadukan’, into the genetic background of the high-yielding but susceptible ‘Mienoyume’. Resistance is controlled by a single recessive gene in a 1.3-Mbp region. We named this gene bsr1 (brown spot resistance 1). The near-isogenic line bsr1-NIL had a greater yield with larger grain width than Mienoyume but similar other agronomic traits in fields where BS was mild; it had a significantly lower BS disease score and a 28.8% higher yield in fields where BS was more severe, and it showed resistance to multiple isolates of BS fungus. It showed stable resistance to BS and had excellent agricultural traits in the presence of BS. We developed the bsr1-NIL with resistance to BS and applied it for variety registration to Ministry of Agriculture, Forestry and Fisheries in Japan as ‘Mienoyume BSL’. This is the first report for the BS resistant rice variety bred using marker-assisted selection.     

Identification and validation of a yield-enhancing QTL cluster in rice (Oryza sativa L.)

Improvement of rice grain yield (YD) is an important goal in rice breeding. YD is determined by its related traits such as spikelet fertility (SF), 1,000-grain weight (TGW), and the number of spikelets per panicle (SPP). We previously mapped quantitative trait loci (QTLs) for SPP and TGW using the recombinant inbred lines (RILs) derived from the crosses between Minghui 63 and Teqing. In this study, four QTLs for SF and four QTLs for YD were detected in the RILs. Comparison of the locations of QTLs for these three yield-related traits identified one QTL cluster in the interval between RM3400 and RM3646 on chromosome 3. The QTL cluster contained three QTLs, SPP3a, SF3 and TGW3a, but no YD QTL was located there. To validate the QTL cluster, a BC₄F₂ population was obtained, in which SPP3a, SF3 and TGW3a were simultaneously mapped to the same region. SPP3a, SF3 and TGW3a explained 36.3, 29.5 and 59.0 % of phenotype variance with additive effect of 16.4 spikelets, 6 % SF and 1.8 g grain weight, respectively. In the BC₄F₂ population, though the region has opposite effects on TGW and SPP/SF, a YD QTL YD3 identified in this cluster region can increase 4.6 g grains per plant, which suggests this QTL cluster is a yield-enhancing QTL cluster and can be targeted to improve rice yield by marker aided selection.     

Tagging quantitative trait loci associated with grain yield and root morphological traits in rice (Oryza sativa L.) under contrasting moisture regimes

Plant breeding for drought-prone habitats envisages a favorable combination of grain yield and drought resistance. Though several components enhancing drought resistance have been identified in rice,their association with grain yield, under low-moisture stress, has been established in very few instances. We attempt to study the associations between rice grain yield and root system parameters both at phenotypic and genotypic levels. The doubled haploid population of IR64/Azucena was evaluated for root related traits at peak vegetative stage and grain yield related traits under both low-moisture stress and non stress conditions. ‘Mean environment’ was computed for yield related traits. Correlation and QTL mapping was attempted to find out the associations. The correlation between maximum root length and grain yield was positive under stress and negative in non stress. Genotypes with thicker and deeper roots, manifested higher biomass and grain yield under stress. Only one QTL found to increase days to flowering in non stress was also found to influence root volume and dry weight negatively under stress. The study suggests that loci enhancing grain yield and related traits were not pleiotropic with loci for desirable root morphological traits studied under low-moisture stress at vegetative stage, in the genetic material used in the study. It is thus possible to combine higher grain yield and desirable root morphological traits, favorably, to enhance productivity of rice under low-moisture stress. In rainfed ecologies, where deep roots contribute to enhanced drought resistance in rice, the results indicate the possibility of combining drought resistance with higher levels of grain yield. This revised version was published online in August 2006 with corrections to the Cover Date.     

Development of high yielding IR64 × <Emphasis Type="Italic">Oryza rufipogon</Emphasis> (Griff.) introgression lines and identification of introgressed alien chromosome segments using SSR markers

Modern rice varieties that ushered in the green revolution brought about dramatic increase in rice production worldwide but at the cost of genetic diversity at the farmers’ fields. The wild species germplasm can be used for broadening the genetic base and improving productivity. Mining of alleles at productivity QTL from related wild species under simultaneous backcrossing and evaluation, accompanied by molecular marker analysis has emerged as an effective plant breeding strategy for utilization of wild species germplasm. In the present study, a limited backcross strategy was used to introgress QTL associated with yield and yield components from Oryza rufipogon (acc. IRGC 105491) to cultivated rice, O. sativa cv IR64. A set of 12 BC₂F₆ progenies, selected from among more than 100 BC₂F₅ progenies were evaluated for yield and yield components. For plant height, days to 50% flowering and tillers/plant, the introgression lines did not show any significant change compared to the recurrent parent IR64. For yield, 9 of the 12 introgression lines showed significantly higher yield (19–38%) than the recurrent parent IR64. Four of these lines originating from a common lineage showed higher yield due to increase in grain weight and another three also from a common lineage showed yield increase due to increase in grain number per panicle. For analyzing the introgression at molecular level all the 12 lines were analyzed for 259 polymorphic SSR markers. Of the total 259 SSR markers analyzed, only 18 (7.0%) showed introgression from O. rufipogon for chromosomes 1, 2, 3, 5, 6 and 11. Graphical genotypes have been prepared for each line and association between the introgression regions and the traits that increased yield is reported. Based on marker trait association it appears that some of the QTL are stable across the environments and genetic backgrounds and can be exploited universally.     

Genetic relationships between anther and stigma traits revealed by QTL analysis in two rice advanced-generation backcross populations

Anther and stigma size are critical floral traits that influence outcrossing in rice (Oryza sativa), a crop that is predominantly self-fertilizing. The efficiency of hybrid rice seed production depends on efficient outcrossing ability of parental lines, which is promoted by increased anther and stigma size. Phenotypic correlations between anther and stigma traits have been observed in many studies; however, evidence for this relationship is unclear and the genetic basis remains to be elucidated. To examine this relationship and to identify quantitative trait loci (QTLs) for increased anther and stigma size, we developed two advanced backcross QTL mapping populations derived from a cross between a Thai elite indica crop variety (SPR1) and an accession of common wild rice (O. rufipogon Griff.), which is predominantly outcrossing. One mapping population was selected for increased anther size while the other was selected for increased stigma size. We mapped QTLs for anther size and stigma size in both populations. Bulked segregant analysis was used to identify molecular markers associated with the selected traits. A total of 16 significant QTLs associated with anther and stigma traits were identified across the two populations, and these were located in five genomic regions on four chromosomes. Whereas three of these regions have been previously reported, two of them are newly identified and should be further explored for improving outcrossing ability in rice. The co-localization of QTL for anther and stigma traits strongly suggests some degree of shared developmental basis for these traits.     

Construction of chromosomal segment substitution lines and genetic dissection of introgressed segments associated with yield determination in the parents of a super‐hybrid rice

Heterosis is a phenomenon whereby hybrids of inbred lines produce favourable phenotypes that exceed those of their parents. Traits of interest are higher yield and stronger stress tolerance. The two‐line super‐hybrid rice ‘Liangyoupei9’ (LYP9) shows superiority to both its elite inbred line ‘93‐11’ and ‘Pei'ai64s’ (‘PA64s’) parents and conventional hybrids. However, the genetic basis of its hybrid vigour, especially yield determination, remains elusive. In the present study, a set of 156 chromosome segment substitution lines (CSSLs) carrying overlapping segments from ‘PA64s’ in a genetic background of ‘93‐11’ were constructed and planted in six environments. Three major agronomic traits, viz. panicle length (PL), heading date (HD) and plant height (PH), and five yield‐related traits, viz. grain weight per panicle (GWP), number of grains per panicle (GPP), 1000‐grain weight (TGW), seed set (SS) and number of panicles of per plant (PPP), were evaluated over 3 years. Quantitative trait loci (QTL) analysis was conducted using a likelihood ratio test based on stepwise regression. Forty‐six putative QTL distributed on 11 chromosomes were detected in more than one year. Remarkably, GWP of four CSSLs carrying positive yield QTL outperformed the recurrent parent ‘93‐11’ by more than 15%, in at least two environments. These results indicate that CSSLs are effective in identifying yield‐associated traits, and lines harbouring such QTL will be rich in resources for future molecular breeding programmes.     

Quantitative trait loci for grain-quality traits across a rice F2 population and backcross inbred lines

Improving grain-quality is an important goal in rice breeding programs. One vital step is to find major quantitative trait loci (QTLs) for quality related traits and then investigate the relationships among them. We crossed ‘N22’, an indica variety with good appearance but low grain weight, to a japonica variety, ‘Nanjing35’, with superior grain yield but poor appearance. This enabled us to construct an F₂ population and a set of backcross inbred lines (BILs) for QTL-mapping for the traits related grain appearance. In all, 37 QTLs were identified for grain length (GL), grain width (GW), grain thickness (GT), thousand-grain weight (TGW), and the percentage of grains with chalkiness (PGWC). Of these, 17 QTLs detected from 184 plants in the F₂ population explained 4.97–27.26 % of the phenotypic variance, another 20 QTLs were identified using BILs from 2009 to 2010. Quantitative trait loci for major effects were detected in different populations and across years. A new QTL hot spot (marker interval RM504–RM520) was found on Chromosome 3, which harbored QTLs for GL, GW, GT, and TGW. Among our five examined traits, grain shape was significantly correlated with TGW and PGWC. The PGWC values of two heavier grains BILs, L93, and L145 are much lower than Nanjiing35, the analysis of genotype showed that this greater weight may due to the locus for GL occurring within RM504–RM520 on Chromosome 3. Therefore, those two lines will allow us to develop a long-grain high-yield rice variety with less chalkiness.     

Upland rice breeding in Brazil: a simultaneous genotypic evaluation of stability, adaptability and grain yield

A durum wheat recombinant inbred line population developed from PDW 233 × Bhalegaon 4 cross was analyzed in five environments to understand the genetic network responsible for test weight (TW), thousand kernel weight (TKW), grain yield (YLD), spike length (SL), spikelets per spike (SPS), kernels per spike (KER) and kernel weight per spike (KWS). Genotype, environment and their interactions were main sources of variance for all the traits. TW and TKW were influenced by 11 main effect QTL and 6 digenic epistatic interactions detected on chromosomes 2A, 2B, 4B and 7A. Grain yield was influenced by three epistatic interactions and five main effect QTL, of which two on chromosome 2A were most consistent. A major QTL for spike length was observed on chromosome 3B. QTL for spike characters were distributed over 9 chromosomes. All the traits showed significant influence of digenic epistasis (QQ) and, to a certain extent, QTL × environment interactions (QQE). Therefore, while breeding for complex traits like kernel characters and grain yield components, these interactions should also be considered important. The consistent QTL on chromosome 2A between the marker interval Xgwm71.2–Xubc835.4 with pleiotropic effect on TW and TKW, may be utilized in early generation selection to improve TW and TKW and thereby the milling potential of the durum wheat.     

Haplotype structure in grain weight gene GW2 and its association with grain characteristics in rice

GW2, a grain weight quantitative trait locus (QTL) in rice encodes a ring type E-3 ubiquitin ligase. A single nucleotide deletion at the 346th nucleotide position in the ligase domain of GW2 was earlier reported to result in higher grain weight in rice. The present study aimed at validating the known functional polymorphism and identifying additional natural genetic variation if any, in the region that included the functional domain of GW2 in a set of indica and aromatic genotypes for which ninety three rice genotypes were phenotyped for grain length, grain width and 100 grain weight. A wide range of variation was observed for these traits. PCR amplification and sequencing of GW2 target region revealed absence of insertion/deletion (InDel) at the 346th position which suggested that the genetic variation in grain weight in Basmati and non-Basmati indica genotypes was not explained by this InDel. However, four new single nucleotide polymorphisms (SNPs) were discovered at nucleotide positions 406, 461, 466 and 501 in the fifth exon and one InDel each in second and fourth introns. Only two of these SNPs, at positions 461 and 501 led to amino acid substitutions. A total of 10 haplotypes were constructed based on these four SNPs which could be regrouped into four categories based on their amino acid substitutions. Association genetic analysis of these haplotypes with different grain traits revealed a moderate association with grain width (R² = 0.18 at P < 0.05). Thirteen haplotypes constructed using both intronic and exonic polymorphisms did not have any association with grain traits.     

Advanced backcross QTL analysis reveals complicated genetic control of rice grain shape in a japonica × indica cross

Grain shape is an important trait for improving rice yield. A number of quantitative trait loci (QTLs) for this trait have been identified by using primary F₂ mapping populations and recombinant inbred lines, in which QTLs with a small effect are harder to detect than they would be in advanced generations. In this study, we developed two advanced mapping populations (chromosome segment substitution lines [CSSLs] and BC₄F₂ lines consisting of more than 2000 individuals) in the genetic backgrounds of two improved cultivars: a japonica cultivar (Koshihikari) with short, round grains, and an indica cultivar (IR64) with long, slender grains. We compared the ability of these materials to reveal QTLs for grain shape with that of an F₂ population. Only 8 QTLs for grain length or grain width were detected in the F₂ population, versus 47 in the CSSL population and 65 in the BC₄F₂ population. These results strongly suggest that advanced mapping populations can reveal QTLs for agronomic traits under complicated genetic control, and that DNA markers linked with the QTLs are useful for choosing superior allelic combinations to enhance grain shape in the Koshihikari and IR64 genetic backgrounds.     

Rapid and high-precision marker assisted backcrossing to introgress the <Emphasis Type="Italic">SUB1</Emphasis> QTL into BR11, the rainfed lowland rice mega variety of Bangladesh

Flooding is one of the major hazards of rice production for the rainfed lowland rice ecosystem, and tolerant cultivars are urgently needed to help protect farmers from submergence damage. A quick and efficient strategy was implemented to introgress SUB1, a major QTL for submergence tolerance, into a rainfed lowland mega variety BR11 of Bangladesh by only two backcrosses and one selfing generation. In marker-assisted backcrossing (MABC), one tightly-linked simple sequence repeat (SSR) and two gene-based markers, four flanking SSR and 116 background SSR markers were used for foreground, recombinant and background selection, respectively, in backcrosses between a SUB1 donor IR40931-33-1-3-2 and BR11. BR11-Sub1, identified in a BC₂F₂ plant, possessed BR11 type SSR alleles on all fragments analyzed except the SUB1 QTL. The introgression size in BR11-Sub1 was 800 Kb indicating approximately 99.8% identity to BR11. BR11-Sub1 along with other introgression lines showed submergence tolerance similar to the tolerant parent. Yield, yield-component parameters and grain physico-chemical properties showed successful recovery of the BR11 traits in BR11-Sub1, with yield potential ranging from 5.2 to 5.6 t/ha, not significantly different from the recurrent parent mega variety BR11. Producing a large number (~1000) of backcross F₁ plants was considered essential to achieve recombination on both sides of the gene, limiting linkage drag with only two backcrosses. A large number of background markers ensured proper recovery of the recurrent parent genome in the BC₂F₂ generation. The study demonstrates a rapid and highly precise strategy to introgress a major QTL by BC₂F₂ generation into a modern rice variety using an unadapted donor. The variety can replace BR11 on more than 2 million of ha in Bangladesh and provide major increases in rice production.     

Analysing genetic control of cooked grain traits and gelatinization temperature in a double haploid population of rice by quantitative trait loci mapping

Cooking quality in rice grains is a complex trait which requires improvement. Earlier reports show varying genetic influence on these traits, except for a common agreement on waxy (Wx) and alkali degeneration (Alk) loci on chromosome 6. The present study involved 86 doubled haploid lines derived from an indica × japonica cross involving IR64 and Azucena. Grain parameters viz., raw grain length (RGL), raw grain breadth (RGB), cooked grain length (CGL), cooked grain breadth (CGB), gelatinization temperature (GT), grain shape (RGS), length elongation ratio (LER) and breadth expansion ratio (BER) were subjected to mixed model mapping of quantitative trait loci (QTL). Segregation data of 175 markers covering a distance of 2395.5 cM spanning the entire genome were used. Fifteen main effect QTLs were detected spread over the genome, except on chromosomes 4, 8 and 11. Thirty epistatic interactions significantly influencing the traits were detected. Twelve of the main effect QTLs were involved in epistatic interactions. One main effect QTL associated with LER was detected near Alk locus. QTLs located for grain length on chromosomes 9 and 10 are reported for the first time. Detection of many epistatic loci and involvement of main effect QTLs in interactions demand for judicious selection of QTLs in marker-assisted selection programmes.     

Development and evaluation of pyramiding lines carrying early or late heading QTLs in the indica rice cultivar ‘IR64’

The heading date is an important trait for determining regional and climatic adaptability in rice. To expand the adaptability of the indica rice cultivar ‘IR64’, we pyramided multiple early or late heading quantitative trait locus (QTLs) in the ‘IR64’ genetic background by crossing previously developed near-isogenic lines (NILs) with a single QTL for early or late heading. The effects of pyramiding QTLs were observed in three different climatic zones of the Philippines, Madagascar, and Japan. The early heading pyramiding lines (PYLs) headed 6.2 to 12.8 days earlier than ‘IR64’ while the late heading PYLs headed 18.8 to 27.1 days later than ‘IR64’. The PYLs tended to produce low grain yield compared to ‘IR64’. The low yield was not improved by combining SPIKE, which is a QTL that increases the number of spikelets per panicle. Conversely, ‘IR64-PYL(7+10)’ carrying Hd5 and Hd1 headed earlier, produced more tillers, and more panicles per m² than ‘IR64’, and mitigated the yield decrease in early heading. These results suggest that the effects of pyramided QTLs on heading date were consistent across various environments and PYLs could be used to enhance the adaptation of ‘IR64’ in other rice growing environments.     

Molecular mapping of quantitative trait loci for plant growth, yield and yield related traits across three diverse locations in a doubled haploid rice population

A doubled haploid (DH) population of 125lines derived from IR64 × Azucena, an indica – japonica cross were grown in three different locations in India during the wet season of 1995. The parents of mapping population had diverse phenotypic values for the eleven traits observed. The DH lines exhibited considerable amount of variation for all the traits. Transgressive segregants were observed. Interval analysis with threshold LOD > 3.00 detected a total of thirty four quantitative trait loci (QTL) for eleven traits across three locations. The maximum number of twenty QTL were detected at Punjab location of North India. A total of seven QTL were identified for panicle length followed by six QTL for plant height. Eight QTL were identified on three chromosomes which were common across locations. A maximum of seven QTL were identified for panicle length with the peak LOD score of 6.01 and variance of 26.80%. The major QTL for plant height was located on Chromosome 1 with peak LOD score of 16.06 flanked by RZ730-RZ801 markers. Plant height had the maximum number of common QTL across environment at the same marker interval. One QTL was identified for grain yield per plant and four QTL for thousand grain weight. Clustering of QTL for different traits at the same marker intervals was observed for plant height, panicle exsertion, panicle number, panicle length and biomass production. This suggests that pleiotropism and or tight linkage of different traits could be the plausible reason for the congruence of several QTL. Common QTL identified across locations and environment provide an excellent opportunity for selecting stable chromosomal regions contributing to yield and yield components to develop QTL introgressed lines that can be deployed in rice breeding program. This revised version was published online in July 2006 with corrections to the Cover Date.     

New quantitative trait loci for enhancing adaptation to salinity in rice from Hasawi,a Saudi landrace into three African cultivars at the reproductive stage

Salinity is a major constraint affecting rice productivity in rainfed and irrigated agro-ecosystems. Understanding salinity effects on rice production at the reproductive stage could improve adaptation for this trait. Identifying quantitative trait loci (QTLs) controlling adaptation to salinity may also accelerate breeding rice germplasm for environments prone to this stress. We used the salt tolerant landrace ‘Hasawi’ as a donor parent to generate three F₂ offspring (consisting each of 500 individuals) with three African cultivars (‘NERICA-L-19’, ‘Sahel 108’ and ‘BG90-2’) used as recipient parents (RP). The F₂s and F_2:3s were evaluated for grain yield and other traits in saline fields. Salinity caused reduction in all measured traits across the F₂-derived offspring, e.g. grain yield reduced between 65 and 73 %, but some offspring had twice the RP’s grain yield. QTL analysis revealed 75 QTLs for different traits in all 3 genetic backgrounds (GBs): 24 of them were common among all the 3 GBs while 31 were noted in 2 GBs, and 17 in one GB. ‘Hasawi’ contributed on average 49 % alleles to these QTLs. Two yield and yield related QTLs (qGY11 and qTN11) common in all 3 GBs were mapped on the same chromosomal segment suggesting these QTLs might be stable across different GBs. Four other QTLs were strongly associated with salinity tolerance with peak marker RM419, representing a potential candidate for MAS due to high LOD score and relatively large effect QTLs.