Genetic studies of speciation in cultivated rice. 5. Inter- and intraspecific differentiation in the waxy gene expression of rice

Summary To get an insight in the gene regulation at the waxy locus of rice, the Wx gene product (Wx protein) controlling the synthesis of amylose was examined by electrophoretic techniques. Among nonwaxy rice strains, two different alleles, Wx ^a and Wx ^b, were found at the waxy locus. Wx ^a drastically enhanced the quantitative level of Wx protein as well as the amylose content in endosperm starch as compared with Wx ^b. The alleles acted additively in triploid endosperms. This implies that regulatory elements responsible for the Wx gene expression are on the same chromosome. The distribution patterns of Wx ^a and Wx ^b in five species of Oryza revealed that the regulatory changes are closely related to racial differentiation within a common rice species (O. sativa), suggesting that Wx ^b might have been selected for through the difference in grain quality during domestication.     

Comparison of Starch Levels Reduced by High Temperature During Ripening in Japonica Rice Lines Near‐Isogenic for the Wx Locus

One problem caused by high temperature during ripening in Japonica rice cultivars is a reduction in the amount of starch in the endosperm. To better understand this deleterious effect, we compared the accumulation of the two components of starch, amylose and amylopectin in grains ripened at high (32/28 °C) and low (22/18 °C) day/night temperatures in a set of lines of Japonica cultivar Taichung 65 (T65Wx^b) that are near‐isogenic for the Wx locus, which encodes granule‐bound starch synthase I. In T65Wx^b ripened at high temperature, the amount of starch per grain decreased. However, amylose per grain significantly decreased while amylopectin per grain significantly increased. On the other hand, the amount of amylopectin in T65wx, the amylose‐free line, did not differ significantly at the high and low temperatures. These data indicated that high temperatures during ripening did not directly affect amylopectin accumulation in T65Wx^b and that the reduction in starch in T65Wx^b from the high temperatures was caused by a decrease only of amylose. The results for T65Wx^a and T65Wx^op were also consistent with this conclusion. As a result of the decrease in amylose, the outer region of starch granules from T65Wx^b ripened at the high temperatures also had less I₂KI staining. Because this fact might suggest that a portion of amylose was synthesized inside the developing granules after amylopectin synthesis in rice, the effect of amylose deposition in increasing of the density of starch granules is also discussed.     

Effects of the two most common Wx alleles on different genetic backgrounds in rice

Wx^a and Wx^b are the most common alleles of the Wx gene in Asian cultivated rice. The difference between them is responsible for differences in the levels of the Wx gene product in the endosperm, as well as in amylose content, which is an important determinant of the quality of edible rice. Since Indica rice mostly carries the Wx^a allele, we introduced the Wx^b allele into Indica‐type rice (IR36) from a Japonica‐type rice (T65) by repeated backcrossing. In the near‐isogenic line (IR36 Wx^b), the level of the Wx gene product was reduced and, as expected, the level of amylose. However, IR36Wx^b had a lower amylose content than the recurrent parent of T65 with the Wx^b allele. The results suggest that the Indica (IR36) background might lower the amylose content more than the Japonica (T65) background when the Wx allele is the same. The possible importance of modifiers that regulate expression of the Wx gene is also discussed in relation to improvements in the grain quality of rice.     

Developing gene-tagged molecular markers for functional analysis of starch-synthesizing genes in rice (Oryza sativa L.)

The granule-bound starch synthase(GBSS), starch branching enzymes 1 (SBE1)and 3 (SBE3) are major enzymes involved in starch biosynthesis in rice endosperm. Available sequences of Sbe1 and Sbe3 genes encoding corresponding SBE1 and SBE3 have been used to identify homologous regions from genome databases of both the indica rice 93-11 and the japonica rice Nipponbare. Sequence diversities were exploited to develop gene-tagged markers to distinguish an indica allele from a japonica allele for both Sbe1 and Sbe3 loci. With these newly developed gene-tagged markers and available Wx gene markers, the roles of these starch-synthesizing genes (Sbe1, Sbe3, and Wx) in determining amylose content (AC) in the rice endosperm were evaluated using a double-haploid (DH)population derived from a cross between the indica rice cv. Nanjing11 and the japonica rice cv. Balilla. Only the Wx and Sbe3 loci had significant effects on the AC variation. On average, indica Wx ^a genotypes showed ∼9.1% higher AC than japonica Wx ^b genotypes, while indica Sbe3 ^a genotypes showed ∼1.0% lower AC than japonica Sbe3 ^b genotypes. A significant interaction was also observed between Wx and Sbe3 loci whereby the amylose content was 0.3% higher in Sbe3 ^a than Sbe3 ^b genotypes in the presence of the Wx ^a allele, but it was lower by 2.3% in the presence of the Wx ^b allele. Overall, polymorphisms at the Wx and Sbe3 loci together could account for 79.1% of the observed AC variation in the DH population. The use of gene-tagged markers in marker-assisted selection and gene functional analysis was also discussed. This revised version was published online in July 2006 with corrections to the Cover Date.     

Amylose synthesis capacity of the three Wx genes of wheat cv. Chinese Spring

The Wx locus controls amylose synthesis in the cereal endosperm. Hexaploid wheat (Triticum aestivum L.) has the three Wx loci on chromosomes 7A ( Wx-A1), 4A (Wx-B1) and 7D (Wx-D1). To verify the effects of null alleles on reducing amylose content and determine the amylose synthesis capacity of each Wx gene independently and accurately, we produced eight possible types of recombinant lines carrying different null alleles at the Wx loci under the ‘Chinese Spring’ genetic background. Amylose content varied from 0% of the waxy ‘Chinese Spring’ to 25% of the ‘Chinese Spring’ normal type. The reducing effect of the single null alleles was the largest in Wx-B1b, and there was no significant difference between Wx-A1b and Wx-D1b. More than 3% reductions in amylose content were detected in the double null types. The results of the double null lines further demonstrated that for the capacity of amylose synthesis, Wx-B1a predominates and produces 21–22% amylose, followed by Wx-D1a (20–21%) and Wx-A1a (15–18%). These significant differences were partly correlated with variation in the amounts of the Wx proteins produced by different Wx genes. However, comparisons of the double null lines with the single null or normal lines indicated that amylose content was not linearly proportional to the number of the Wx genes, suggesting that the Wx genes act in an epistatic manner. This revised version was published online in July 2006 with corrections to the Cover Date.     

Influence of single-nucleotide polymorphisms in the gene encoding granule-bound starch synthase I on amylose content in Vietnamese rice cultivars

Amylose content is one of the most important factors influencing the physical and chemical properties of starch in rice. Analysis of 352 Vietnamese rice cultivars revealed a wide range of variation in apparent amylose content and the expression level of granule-bound starch synthase. On the basis of single-nucleotide polymorphisms (SNP) at the splicing donor site of the first intron and in the coding region of the granule-bound starch synthase I gene, Waxy gene, alleles can be classified into seven groups that reflect differences in apparent amylose content. The very low and low apparent amylose content levels were tightly associated with a G to T in the first intron whereas intermediate and high amylose was associated with a T genotype at SNP in exon 10. The correlation between the combination of T genotype at SNP in the first intron, C in exon 6, or C in exon 10 was predominant among low amylose rice varieties. Our analysis confirmed the existence of Wx^op allele in Vietnamese rice germplasm. The results of this study suggest that the low amylose properties of Vietnamese local rice germplasm are attributable to spontaneous mutations at exons, and not at the splicing donor site.     

水稻Wx复等位基因基于PCR的功能标记开发与利用

直链淀粉含量是影响稻米食味品质的重要因素,主要由蜡质基因(Wx)调控,Wx基因座存在Wxa、Wxb、Wxin、Wxmw等多个复等位基因,通过分子标记辅助选择(marker-assisted selection,MAS)培育中低直链淀粉含量的水稻品种是提高稻米适口性的重要途径。Wx复等位基因的功能由单碱基核苷酸多态性(single nucleotide polymorphisms,SNP)决定,其检测依赖于测序或酶切,存在耗时多、费用昂贵等缺点。为提高选择效率,本文利用Wx复等位基因的SNP差异和四引物扩增受阻突变(tetra-primer ARMS-PCR)原理,进行PCR功能标记的开发。引物设计过程中,针对扩增效率低和非匹配的延伸2个技术难题,提出了调整错配位点的解决方案,成功开发了基于PCR技术的两对功能性标记Waxygt-ARMS2和Waxyac-ARMS2,可以准确区分上述复等位基因型,且具有操作简单、耗费较低的特点。利用新开发标记对辽宁省育成的部分水稻品种进行Wx基因型检测的结果表明,40份辽宁育成品种均携带Wxb基因,遗传基础单一。上述结果为利用Wx基因位点的分子标记培育中低直链淀粉含量的水稻品种,改良辽宁省水稻品种的食味品质提供了技术支撑。     

Identification of allelic variations of puroindoline genes controlling grain hardness in wheat using a modified denaturing PAGE

The amount of long chains (LC) of amylopectin in high-amylose rice is thought to be one of the important determinants of its quality when cooked. A wide range of differences in LC content have been reported in rice varieties, which can be clearly divided into four classes based on LC and apparent amylose content: namely, amylose and LC-free, low or medium-amylose and low-LC, high-amylose and medium-LC, high-amylose and high-LC. However, genetic factors controlling LC content have not been fully understood. Here, we performed quantitative trait loci (QTL) analysis of LC content using 157 recombinant inbred lines (RILs) derived from a cross of a low-LC cultivar, Hyogokitanishiki, and a high-LC line, Hokuriku 142. By analyzing randomly selected 15 RILs, it was shown that high LC content (≥11%) was associated with high setback viscosity (≥200 RVU), and that low LC (≤ 3%) was associated with low setback viscosity (≤ 130 RVU), as measured by a Rapid Visco Analyzer. With setback viscosity as an indicator for LC content, QTL analysis was conducted using 60 DNA markers including a CAPS marker that distinguished Wx a and Wx b alleles coding for granule-bound starch synthase I (GBSSI or Wx protein), the enzyme working for amylose biosynthesis. Only one QTL with a peak log of likelihood score at the wx locus was detected, and no line showing setback viscosity corresponding to the medium-LC class appeared. The fact that wx mutants of Hokuriku 142 lacked LC in their rice starch supports the view that the functional Wx allele is indispensable for LC synthesis in addition to amylose synthesis in rice endosperm. We suggest three possible reasons why no line with medium-LC content was observed. First, the locus (loci) responsible for generation of medium-LC may be located very close to the wx locus and not able to be dissected by the population and DNA markers we used. Second, there may be special QTLs for medium-LC cultivars that do not exist in low- or high-LC cultivars. Third, medium-LC cultivars may have an as-yet unidentified Wx allele with lower capability in LC synthesis compared to the Wx allele in high-LC cultivars.     

Isolation and characterization of a rice mutant insensitive to cool temperatures on amylose synthesis

The Wx ^b gene, one of the alleles at the rice waxy(wx) locus, is activated at cool temperatures during seed development, andas a result, a large amount of amylose is accumulated causing a reductionin rice grain quality. We found that the seeds of a du mutant couldbe visibly distinguished depending on whether they matured at cool ornormal temperatures. Using these characteristics, we isolated a mutantcandidate insensitive to cool temperatures. While the amylose content inthe original line was about 2% at a normal temperature (28 °C)and 12% at a cool temperature (21 °C), in the mutant candidate(coi) the amylose content was not affected by temperatures, i.e. theamylose content was about 3% at both temperatures. This finding incombination with the results of an immunoblot analysis indicated that theabsence of an increase in the amylose content in this mutant was caused bya constant level of Wx gene expression at normal and cooltemperature. Genetic analysis revealed that this insensitivity to cooltemperatures was caused by a single recessive mutation. This mutantshould be useful in breeding programs designed to produce rice of desiredquality at cool temperatures and in understanding genetic and molecularmechanisms that respond to slight changes in temperature.     

Gene dosage effect of the wheat Wx alleles and their interaction on amylose synthesis in the endosperm

To find out gene dose effect of each of the three homoeologous Wx genes and their interaction on the production of granule-bound starch synthase (GBSS I) and amylose biosynthesis in the endosperm, Chinese Spring and its near-isogenic waxy types were crossed reciprocally and, obtained a plant population with varying doses of each Wx gene. The amount of GBSSI was increased linearly with increasing gene dose of either of Wxloci. In each of the three Wx loci, the change in amylose content was linear up to 3 doses, with a more potent capacity ofWx-B1a at any dose. Higher level of amylose production was observed in the reciprocal F₁ grains than the expected effect of dose/s of each gene or additive effect of different allelic combination by artificially blend starches which have amylose produced by equivalent number ofWx alleles to that of relevant F₁ cross. When Wx-B1a and Wx-A1a were combined, increase in amylase content was not in proportion to increase in gene dosage. The enhanced amylase synthesis was shown by 2-gene and 3-geneinteraction, indicating that not only type of the three Wx genes and its dose but the interaction among them have significant roles in determining the amylose content. This revised version was published online in July 2006 with corrections to the Cover Date.     

Characterization of waxy grain sorghum lines in relation to granule-bound starch synthase

The waxy phenotype, associated with endosperm containing little or no amylose, has been recognized in sorghum (Sorghum bicolor L. Moench) since 1933. Although variants of the waxy gene are well characterized in other cereals, the waxy trait has been assumed to be controlled by a single allele, wx, in sorghum. Recent improvements in technologies encourage re-examination of the waxy sorghums. The objectives of this research were therefore to identify and characterize sorghum lines with differing waxy alleles and to describe the actions of those alleles in crosses. Grain of eight waxy sorghum lines (BTxARG1, BTx630, Tx2907, B.9307, 94C274, 94C278, 94C289, 94C369), three wild-type checks (BWheatland, RTx430, BN122), and F₂ families from crosses among a subset of these lines were evaluated for presence or absence of granule-bound starch synthase (GBSS), the gene product of the wx locus, and wild-type vs. waxy endosperm. The F₂ segregation ratios were tested for fit to a 3:1 ratio using Chi-square analyses. Two distinctly different naturally occurring waxy alleles were identified: One with no GBSS (GBSS−), and one with apparently inactive GBSS present (GBSS+). We propose that the waxy allele with no GBSS be designated wx^a, and that waxy allele with apparently inactive GBSS present be designated wx^b. These two alleles are located in close proximity on the waxy locus. The wx^b allele is dominant to the wx^a allele in terms of GBSS production, and both are recessive to the wild-type Wx in terms of amylose content. The U.S. Government's right to retain a non-exclusive, royalty-free license in and to any copyright is acknowledged.     

Variation of <Emphasis Type="Italic">Wx</Emphasis> microsatellite allele,waxy allele distribution and differentiation of chloroplast DNA in a collection of Thai rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.)

Eighty-two varieties of rice from different regions in Thailand were selected to explore the Waxy (Wx)gene diversity and indica-japonica differentiation of chloroplast DNA. A comparison of the 5 splice site in the first intron was made between glutinous and nonglutinous rice. It revealed that non-glutinous with low-amylose content and glutinous rice were characterized as the Wx^b allele based on the G-to-T base substitution, whereas non-glutinous rice with intermediate and high amylose carried the Wx^a allele. Four Wx microsatellite alleles, (CT)_n repeat, (n = 16,17,18 and 19) were found in glutinous rice. In contrast, non-glutinous rice showed five Wx microsatellite alleles (n = 11, 16, 17, 18 and 19). The (CT)₁₇ allele was prominent allele in Thai population, while the (CT)₁₁ allele was found only in intermediate and high amylose rice varieties from southern Thailand. Almost all of upland rice grown by various ethnic groups in northern Thailand were characterized as japonica type based on their having the PstI-12 fragment in their cpDNA, whereas most of rainfed lowland varieties from other regions of Thailand were indica. This exploration of DNA-based genetic markers is important, as it enhances our ability to describe and manipulate sources of genetic variation for rice breeding programs.     

SNPs and an insertion sequence in five Wx-A1 alleles as factors for variant Wx-A1 protein in wheat

The waxy (Wx) gene encodes a granule-bound starch synthase (also called Wx protein) that is involved in synthesizing amylose in the starch grains of cereals, including common wheat (Triticum aestivum L.). Because amylose content affects the quality of food products made from wheat flour, Wx alleles affecting amylose content are of interest. Five wheat Wx alleles (Wx-A1c, -A1d, -A1e, -A1i and -A1j) that produce polymorphic Wx proteins on electrophoretic gels were investigated in terms of amylose content in starch and DNA sequences. Measurement and electrophoresis of gelled starch showed that apparent amylose contents of the genotypes were as follows: Wx-A1e, 2.9 % (= waxy phenotype) < -A1i, 8.0 % < -A1c, 16.8 % < -A1j, 22.6 % = level of wild type allele -A1a. DNA sequencing of the five alleles identified single nucleotide polymorphisms (SNPs) and insertion/deletion variations compared to Wx-A1a. A particular SNP causing amino acid changes in Wx-A1e and -A1c was identified as the factor responsible for decreased amylose. A SNP in Wx-A1d should cause an amino acid change and be responsible for an altered Wx-A1d protein. A transposable-like element of 376 bp present in the 3′ untranslated region (UTR) of Wx-A1i most likely lowered the levels of Wx protein and amylose through aberrant mRNA. The fifth allele, Wx-A1j, possessed four SNPs, two of which altered amino acids in the Wx-A1j protein and should cause polymorphism in the Wx protein. Based on the DNA sequences, functional markers for Wx-A1c, -A1d, -A1e and -A1i were developed.     

从携带S5n基因的水稻种质中发掘San、Sbn和Scn基因

花粉不育是籼粳杂种F₁优势利用的主要障碍之一。包括S_a、S_b和S_c等至少6个基因座位内的等位基因互作会引起花粉不育,这些座位上的中性等位基因可以克服不育性。所以,发掘和利用中性等位基因具有重要意义。本文用携带S₅ⁿ的水稻种质,分别与台中65及其携带花粉不育基因的一套近等基因系杂交,组配具有单个座位互作和多个座位同时互作的杂种F₁,首先通过观察杂种F₁的花粉育性并比较相应杂种F₁育性的差异,初步判断是否具有中性等位基因,然后,采用与S_a、S_b和S_c座位紧密连锁的分子标记对F₂植株基因型的分离进行检测,并分析其分离比例的符合度,确定存在中性等位基因的真实性。结果发现在所鉴定的6份材料中有2份(灰背子和Madhukar)同时携带S_aⁿ和S_bⁿ,3份(饭毫皮、秕五升和粤泰B)携带S_bⁿ,1份(Jackson)携带S_cⁿ。这些材料同时携带可克服杂种F₁胚囊不育和花粉不育的基因,是克服籼粳杂种F₁不育性的重要基因来源。     

Yield and quality evaluations on a pair of processing tomato lines nearly isogenic for the Tm2a gene for resistance to the tobacco mosaic virus

A pair of processing tomato (Lycopersicon esculentum Mill.) lines, nearly isogenic for the Tm-2^a gene for resistance to tobacco mosaic virus, were grown in replicated trials under commercial production conditions in five locations worldwide. The lines were evaluated for 17 processing traits including fruit yield, size, soluble solids concentration, color, firmness, and viscosity. Eight of those traits differed significantly among the nearly-isogenic lines (NILs). Most notably, the NIL heterozygous for Tm-2^a yielded, on average, 16% more than the NIL homozygous for the susceptible allele and 33% more than the NIL homozygous for Tm-2^a. Viscosity was lower in the heterozygous NIL and the homozygous and heterozygous resistant NILs had softer fruit with larger stem scars compared to the homozygous susceptible NIL. These results indicate the presence of the Tm-2^a locus affects many traits of importance for processing tomatoes and may be used, in the heterozygous state, to significantly increase yield. Whether the observed effects are due to the Tm-2^a gene itself or genes associated via linkage drag could not be determined. This revised version was published online in July 2006 with corrections to the Cover Date.     

Amylose content and starch properties generated by five variant <Emphasis Type="Italic">Wx</Emphasis> alleles for granule-bound starch synthase in common wheat (<Emphasis Type="Italic">Triticum aestivum</Emphasis> L.)

In common and durum wheats (Triticum aestivum L. and T. durum Desf.), variant waxy (Wx) alleles have been reported for three Wx proteins (Wx-A1, -B1 and -D1), responsible for amylose synthesis in flour starch. Five variant alleles, Wx-A1c, -A1e, -B1c, -B1d and -D1c, were examined to elucidate their effects on amylose content in flour starch. Common wheat lines carrying a Wx protein produced by one variant (e.g., Wx-A1c) and one control (e.g., Wx-A1a) allele were bred and their starches were compared. Results showed that Wx-A1e did not produce amylose (waxy phenotype), whereas three alleles (Wx-A1c, -B1c and -B1d) reduced amylose, and -D1c might have increased it slightly. Most data on blue value, swelling power and starch paste clarity in water and dimethyl sulphoxide also suggested the variant Wx alleles either reduced or increased amylose content.     

Development of near-isogenic lines of wheat carrying different null Wx alleles and their starch properties

The granule-bound starch synthase (GBSS I) encoded by the Wxgenes, is involved in amylose synthesis. For analyses of mechanisms of amylose synthesis and associated starch properties in hexaploid wheat, eight possible genotypes having different combinations of the three null alleles at the Wx loci with a common genetic background are a prerequisite. A near-isogenic population of doubled haploid (DH) lines was produced from Chinese Spring × waxy Chinese Spring F₁ plants using the wheat × maize method. The Wx protein phenotypes of the DH progeny were examined by sodium dodecyl sulphate-polyacrylamide gel electrophoresis and found that the null alleles at each of the three Wx loci segregated in a Mendelian fashion. A field trial demonstrated no differences between the eight types for ear emergence time, plant height and grain yield traits. Amylose content in the endosperm starch was highest in the wild type while lowest in the waxy type having no Wx proteins. Comparison between single null types and double null types indicated that the amylose synthesis capacity of Wx-A1a allele is the lowest. Pasting properties of starch are the highest in the waxy type, followed by the double null types. Consequently, both peak viscosity and breakdown were negatively correlated with amylose content. The chain-length distribution analysis of amylopectin structure revealed no clear difference among the eight types,suggesting that the reduced GBSS I activity due to introgression of the null Wx alleles does not affect either the chain length or the degree of branching of amylopectin. This revised version was published online in July 2006 with corrections to the Cover Date.     

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.     

A gametocidal factor of Oryza glaberrima Steud. in O. sativa L.

Summary Recurrent backcrossing has been carried out with a view to transfer a gene for non-glutinous endosperm from two strains of O. glaberrima (Wx _g /Wx _g ) to glutinous japonica and indica varieties (wx/wx) of Oryza sativa. In the course of backcrosses Wx _g /wx segregants were crossed with each of the two glutinous varieties of sativa as the respective recurrent male parent. The wx/wx and Wx _g /wx segregants in the successive generations were consistently fully fertile and semi-sterile, respectively. The semi-sterility of Wx _g /wx plants was attributable to abortion of most of the pollen grains carrying the gene wx. The nucleus but not cytoplasm was related to the semi-sterility. The Wx _g /Wx plants having the gene for non-glutinous endosperm of a glaberrima strain and a japonica variety of sativa were also semi-sterile. Both wx- and Wx-megaspores in the plants heterozygous for the gene Wx _g were deleteriously affected. The results could be explained by assuming that a factor tightly linked with the gene Wx _g of glaberrima sterilizes gametes not carrying it in the heterozygotes and that the gametocidal action is exerted when combined with the sativa nucleus by the recurrent backcross method.     

Effects of reduced height (<Emphasis Type="Italic">Rht</Emphasis>) and photoperiod insensitivity (<Emphasis Type="Italic">Ppd</Emphasis>) alleles on yield of wheat in contrasting production systems

Near isogenic lines (NILs) varying for reduced height (Rht) and photoperiod insensitivity (Ppd-D1) alleles in a cv. Mercia background (rht (tall), Rht-B1b, Rht-D1b, Rht-B1c, Rht8c+Ppd-D1a, Rht-D1c, Rht12) were compared for interception of photosynthetically active radiation (PAR), radiation use efficiency (RUE), above-ground biomass (AGB), harvest index (HI), height, weed prevalence, lodging and grain yield, at one field site but within contrasting (‘organic’ vs. ‘conventional’) rotational and agronomic contexts, in each of 3 years. In the final year, further NILs (rht (tall), Rht-B1b, Rht-D1b, Rht-B1c, Rht-B1b+Rht-D1b, Rht-D1b+Rht-B1c) in Maris Huntsman and Maris Widgeon backgrounds were added together with 64 lines of a doubled haploid (DH) population [Savannah (Rht-D1b) × Renesansa (Rht-8c+Ppd-D1a)]. There were highly significant genotype × system interactions for grain yield, mostly because differences were greater in the conventional system than in the organic system. Quadratic fits of NIL grain yield against height were appropriate for both systems when all NILs and years were included. Extreme dwarfing was associated with reduced PAR, RUE, AGB, HI, and increased weed prevalence. Intermediate dwarfing was often associated with improved HI in the conventional system, but not in the organic system. Heights in excess of the optimum for yield were associated particularly with reduced HI and, in the conventional system, lodging. There was no statistical evidence that optimum height for grain yield varied with system although fits peaked at 85 and 96 cm in the conventional and organic systems, respectively. Amongst the DH lines, the marker for Ppd-D1a was associated with earlier flowering, and just in the conventional system also with reduced PAR, AGB and grain yield. The marker for Rht-D1b was associated with reduced height, and again just in the conventional system, with increased HI and grain yield. The marker for Rht8c reduced height, and in the conventional system only, increased HI. When using the System × DH line means as observations grain yield was associated with height and early vegetative growth in the organic system, but not in the conventional system. In the conventional system, PAR interception after anthesis correlated with yield. Savannah was the highest yielding line in the conventional system, producing significantly more grain than several lines that out yielded it in the organic system.