Comparison of QTL controlling seedling vigour under different temperature conditions using recombinant inbred lines in rice (Oryza sativa)

BACKGROUND AND AIMS: Seedling vigour is one of the major determinants for stable stand establishment in rice (Oryza sativa), especially in a direct seeding cropping system. The objectives of this study were to identify superior alleles with consistent effects on seedling vigour across different temperature conditions and to investigate genotype x environmental temperature interactions for seedling vigour QTL. METHODS: A set of 282 F13 recombinant inbred lines (RILs) derived from a rice cross were assessed for four seedling vigour traits at three temperatures (25 degrees C, 20 degrees C and 15 degrees C). Using a linkage map with 198 marker loci, the main-effect QTL for the traits were mapped by composite interval mapping. KEY RESULTS: A total of 34 QTL for the four seedling vigour traits were identified. Of these QTL, the majority (82%) were clustered within five genomic regions, designated as QTL qSV-3-1, qSV-3-2, qSV-5, qSV-8-1 and qSV-8-2. All of these five QTL had small individual effects on the traits, explaining 3.1-15.8 % of the phenotypic variation with a mean of 7.3 %. QTL qSV-3-1, qSV-3-2 and qSV-8-1 showed almost consistent effects on the traits across all three temperatures while qSV-5 and qSV-8-2 had effects mainly at the 'normal' temperatures of 20 degrees C and 25 degrees C. Among the five QTL identified, all and four showed additive effects on shoot length and germination rate, respectively. The contributions of these five QTL to shoot length and germination rate were also much larger than those to the other two traits. CONCLUSIONS: A few of genomic regions (or QTL) were identified as showing effects on seedling vigour. For these QTL, significant genotype x environmental temperature interactions were found and these interactions appeared to be QTL-specific. Among the four seedling vigour traits measured, shoot length and germination rate could be used as relatively good indicators to evaluate the level of seedling vigour in rice.     

Early changes of gene activity in developing seedlings of Arabidopsis hybrids relative to parents may contribute to hybrid vigour

Hybrid vigour (heterosis) has been used for decades in crop industries, especially in the production of maize and rice. Hybrid varieties usually exceed their parents in plant biomass and seed yield. But the molecular basis of hybrid vigour is not fully understood. In this project, we studied heterosis at early stages of seedling development in Arabidopsis hybrids derived from crossing Ler and C24 accessions. We found that early heterosis is associated with non‐additive gene expression that resulted from earlier changes in gene expression in the hybrids relative to the parents. The non‐additively expressed genes are involved in metabolic pathways, including photosynthesis, critical for plant growth. The early increased expression levels of genes involved in energy production in hybrids is associated with heterosis in the young seedlings that could be essential for biomass heterosis at later developmental stages of the plant.     

化学药剂对水稻种子萌发和幼苗生长的影响

以早丰 11号水稻种子为材料 ,用KNO3、KH2 PO4 、Na2 HPO4 等不同药液浸种 .结果显示 ,早丰 11号种子在适当浓度的KNO3、KH2 PO4 、Na2 HPO4 浸种后 ,发芽势、发芽率比对照有所提高 ,幼苗生长加快 ,表现在根长、发根数、苗高、鲜重比对照生长好 ,并且对水稻秧苗表现有抵抗低温的作用 .     

New insights into the genetic basis of natural chilling and cold shock tolerance in rice by genome‐wide association analysis

In order to understand cold adaptability and explore additional genetic resources for the cold tolerance improvement of rice, we investigated the genetic variation of 529 rice accessions under natural chilling and cold shock stress conditions at the seedling stage using genome‐wide association studies; a total of 132 loci were identified. Among them, 12 loci were common for both chilling and cold shock tolerance, suggesting that rice has a distinct and overlapping genetic response and adaptation to the two stresses. Haplotype analysis of a known gene OsMYB2, which is involved in cold tolerance, revealed indica–japonica differentiation and latitude tendency for the haplotypes of this gene. By checking the subpopulation and geographical distribution of accessions with tolerance or sensitivity under these two stress conditions, we found that the chilling tolerance group, which mainly consisted of japonica accessions, has a wider latitudinal distribution than the chilling sensitivity group. We conclude that the genetic basis of natural chilling stress tolerance in rice is distinct from that of cold shock stress frequently used for low‐temperature treatment in the laboratory and the cold adaptability of rice is associated with the subpopulation and latitudinal distribution.     

Genome-wide association mapping of salinity tolerance in rice (Oryza sativa)

Salinity tolerance in rice is highly desirable to sustain production in areas rendered saline due to various reasons. It is a complex quantitative trait having different components, which can be dissected effectively by genome-wide association study (GWAS). Here, we implemented GWAS to identify loci controlling salinity tolerance in rice. A custom-designed array based on 6,000 single nucleotide polymorphisms (SNPs) in as many stress-responsive genes, distributed at an average physical interval of <100 kb on 12 rice chromosomes, was used to genotype 220 rice accessions using Infinium high-throughput assay. Genetic association was analysed with 12 different traits recorded on these accessions under field conditions at reproductive stage. We identified 20 SNPs (loci) significantly associated with Na⁺/K⁺ ratio, and 44 SNPs with other traits observed under stress condition. The loci identified for various salinity indices through GWAS explained 5–18% of the phenotypic variance. The region harbouring Saltol, a major quantitative trait loci (QTLs) on chromosome 1 in rice, which is known to control salinity tolerance at seedling stage, was detected as a major association with Na⁺/K⁺ ratio measured at reproductive stage in our study. In addition to Saltol, we also found GWAS peaks representing new QTLs on chromosomes 4, 6 and 7. The current association mapping panel contained mostly indica accessions that can serve as source of novel salt tolerance genes and alleles. The gene-based SNP array used in this study was found cost-effective and efficient in unveiling genomic regions/candidate genes regulating salinity stress tolerance in rice.     

不同类型稻种资源对稗草化感潜力差异评价

以120份不同类型稻种资源为研究对象,将田间鉴定和室内叶浸提液处理鉴定方法相结合,对其化感作用差异进行了鉴定评价.结果表明,在田间不同类型稻种资源对稗草生长的抑制效果大小趋势为地方品种＞选育品种(系)＞引进品种(系)＞杂交水稻(恢复系和不育系),对稗草苗鲜重和苗干重的抑制效果大于对苗高的抑制效果.室内叶浸提液处理鉴定结果,不同类型稻种资源间化感作用差异相对较小,但仍以地方品种较强,并对稗草根长的抑制效果大于对稗草苗高的抑制效果.地方品种中具有较强化感作用的种质资源频率高于其他类型品种,今后要加强对地方品种资源的化感潜力鉴定和评价.     

Allelopathic effects of nicotine on maize I. Its possible importance in crop rotation

Nicotine adversely affected the germination, germination relative index (GRI), radicle and plumule length, and seedling vigour of rice but affected favourably the growth of maize. Also, inin vivo conditions nicotine increased height, specific leaf weight and chlorophyll content of the maize plant.     

Mapping quantitative trait loci for seedling vigor in rice using RFLPs

Improving seedling vigor is an important objective of modern rice (Oryza saliva L.) breeding programs. The purpose of this study was to identify and map quantitative trait loci (QTL) underlying seedling vigor-related traits using restriction fragment length polymorphisms (RFLPs). An F₂ population of 204 plants was developed from a cross between a low-vigor japonica cultivar Labelle (LBL) and a high-vigor indica cultivar Black Gora (BG). A linkage map was constructed of 117 markers spanning 1496 Haldane cM and encompassing the 12 rice chromosomes with an average marker spacing of 14 cM. The length of the shoots, roots, coleoptile and mesocotyl were measured on F₃ families in slantboard tests conducted at two temperatures (18° and 25°C). By means of interval analysis, 13 QTLs, each accounting for 7% to 38% of the phenotypic variance, were identified and mapped in the two temperature regimes at a log-likelihood (LOD) threshold of 2.5. Four QTLs controlled shoot length, 2 each controlled root and coleoptile lengths and 5 influenced mesocotyl length. Single-point analysis confirmed the presence of these QTLs and detected additional loci for shoot, root and coleoptile lengths, these latter usually accounting for less than 5% of the phenotypic variation. Only 3 QTLs detected both by interval and singlepoint analyses were expressed under both temperature regimes. Additive, dominant and overdominant modes of gene action were observed. Contrary to what was predicted from parental phenotype, the low-vigor LBL contributed 46% of the positive alleles for shoot, root and coleoptile lengths. Positive alleles from the high-vigor parent BG were identified for increased root, coleoptile and mesocotyl lengths. However, BG contributed alleles with only minor effects for shoot length, the most important determinant of seedling vigor in water-seeded rice, suggesting that it would not be an ideal donor parent for introducing faster shoot growth alleles into temperate japonica cultivars.     

播种深度对夏玉米幼苗性状和根系特性的影响

选用郑单958(ZD958)和先玉335(XY335)为试验材料,在砂培和大田条件下设置3、5、7和9 cm 4个播种深度,并在大田条件下以不同播种深度混播作为对照(CK),研究播种深度对夏玉米幼苗性状和根系特性的影响.结果表明： 随着播种深度的增加,夏玉米的出苗率下降,出苗时间延长.ZD958和XY335播深9 cm的出苗率较3 cm的分别降低9.4%和11.8%,出苗时间较3 cm的均延长1.5 d.随着播种深度的增加,幼苗长度及幼苗整齐度显著降低,中胚轴长度显著增加,胚芽鞘长度差异不显著;初生胚根长度逐渐减小,次生胚根总长度逐渐增加,总根长度差异不显著;幼苗与中胚轴的总干质量增加,总根干质量差异不显著.随播种深度的增加,种子萌发时幼苗各部位可溶性糖含量增加,营养物质消耗量增加,幼苗根系生长速度增加,根系活力降低,总节根数及节根层数增加.播深增加后出苗率及幼苗活力的降低导致收获穗数的显著降低,最终影响产量形成.此外,播深一致有利于群体整齐度的提高和群体性状的改善,从而提高产量.     

Genetic Diversity and Population Structure in Aromatic and Quality Rice (Oryza sativa L.) Landraces from North-Eastern India

The North-eastern (NE) India, comprising of Arunachal Pradesh, Assam, Manipur, Meghalaya, Mizoram, Nagaland, Sikkim and Tripura, possess diverse array of locally adapted non-Basmati aromatic germplasm. The germplasm collections from this region could serve as valuable resources in breeding for abiotic stress tolerance, grain yield and cooking/eating quality. To utilize such collections, however, breeders need information about the extent and distribution of genetic diversity present within collections. In this study, we report the result of population genetic analysis of 107 aromatic and quality rice accessions collected from different parts of NE India, as well as classified these accessions in the context of a set of structured global rice cultivars. A total of 322 alleles were amplified by 40 simple sequence repeat (SSR) markers with an average of 8.03 alleles per locus. Average gene diversity was 0.67. Population structure analysis revealed that NE Indian aromatic rice can be subdivided into three genetically distinct population clusters: P1, joha rice accessions from Assam, tai rices from Mizoram and those from Sikkim; P2, chakhao rice germplasm from Manipur; and P3, aromatic rice accessions from Nagaland. Pair-wise F_ST between three groups varied from 0.223 (P1 vs P2) to 0.453 (P2 vs P3). With reference to the global classification of rice cultivars, two major groups (Indica and Japonica) were identified in NE Indian germplasm. The aromatic accessions from Assam, Manipur and Sikkim were assigned to the Indica group, while the accessions from Nagaland exhibited close association with Japonica. The tai accessions of Mizoram along with few chakhao accessions collected from the hill districts of Manipur were identified as admixed. The results highlight the importance of regional genetic studies for understanding diversification of aromatic rice in India. The data also suggest that there is scope for exploiting the genetic diversity of aromatic and quality rice germplasm of NE India for rice improvement.     

海南普通野生稻稻瘟病抗性资源调查和鉴定

为挖掘海南普通野生稻稻瘟病抗性资源,2010年诱发鉴定了41个居群410份材料苗期叶瘟,2011年接种稻瘟病菌（YC25）鉴定了37个居群121份材料穗颈瘟,2012年调查了80个居群2461份材料田间自然状态的抗病性。结果表明：苗期叶瘟抗性鉴定有21份高抗、117份抗病。苗期抗、高抗叶瘟性的138份材料中穗颈瘟鉴定4份高抗和3份抗病,14份表现为田间自然抗病。苗期叶瘟鉴定不抗病或未作此鉴定材料中,4份表现为抗穗颈瘟和田间自然抗病。这些抗性材料来自海口、文昌、万宁、三亚、澄迈、东方等地。本研究为海南普通野生稻资源进一步研究和抗稻瘟病育种利用提供参考     

Wet-dry cycling extends seed persistence by re-instating antioxidant capacity

Seeds in the field experience wet-dry cycling that is akin to the well-studied commercial process of seed priming in which seeds are hydrated and then re-dried to standardise their germination characteristics. To investigate whether the persistence (defined as in situ longevity) and antioxidant capacity of seeds are influenced by wet-dry cycling, seeds of the global agronomic weed Avena sterilis ssp. ludoviciana were subjected to (1) controlled ageing at 60% relative humidity and 53.5°C for 31 days, (2) controlled ageing then priming, or (3) ageing in the field in three soils for 21 months. Changes in seed viability (total germination), mean germination time, seedling vigour (mean seedling length), and the concentrations of the glutathione (GSH) / glutathione disulphide (GSSG) redox couple were recorded over time. As controlled-aged seeds lost viability, GSH levels declined and the relative proportion of GSSG contributing to total glutathione increased, indicative of a failing antioxidant capacity. Subjecting seeds that were aged under controlled conditions to a wet-dry cycle (to ?1 MPa) prevented viability loss and increased GSH levels. Field-aged seeds that underwent numerous wet-dry cycles due to natural rainfall maintained high viability and high GSH levels. Thus wet-dry cycles in the field may enhance seed longevity and persistence coincident with re-synthesis of protective compounds such as GSH.     

Seed vigour contributes to yield improvement in dry direct‐seeded rainfed lowland rice

Dry direct‐seeded rice (DSR) cultivation is widely spreading in tropical Asia, but drought and nutrient deficiency stresses often cause crop failure in rainfed lowlands. The objective of this study was to dissect the physio‐morphological characteristics associated with crop establishment and early vigour of DSR under drought and P deficiency conditions in the Philippines. It was found that new drought‐resistant cultivars bred for DSR (Rc348 and Rc192) had faster germination and sprout growth than popular irrigated rice cultivars (Rc222 and Rc10) under soil water deficit due to rapid moisture acquisition by the germinating seeds from drying soils. There was a significant correlation between seed moisture content and the reduction in seed dry weight, and between reduction in seed dry weight and shoot elongation under both control and drought stress treatments at the germination stage. At the seedling stage, the root growth of Rc348 under drought tended to be more vigorous with its higher root‐to‐shoot ratio compared to Rc222 and Rc10. The seedling vigour of Rc348 under P deficiency was also greater than that of Rc222 due to its greater root growth and P uptake. The yields of Rc348 and Rc192 grown under rainfed condition at the target drought‐prone site where a dry spell of 13 days occurred during crop establishment were higher (4.0–4.1 t ha^?1) than the yield of Rc10 (3.0 t ha^?1). These results suggest that quick germination and seedling vigour with quick root anchorage and great nutrient uptake capacity, even with limitations of soil moisture and nutrients, would be important traits for DSR in rainfed lowlands.     

Elongated mesocotyl1, a phytochrome-deficient mutant of maize

To begin the functional dissection of light signal transduction pathways of maize (Zea mays), we have identified and characterized the light-sensing mutant elm1 (elongated mesocotyl1). Seedlings homozygous for elm1 are pale green, show pronounced elongation of the mesocotyl, and fail to de-etiolate under red or far-red light. Etiolated elm1 mutants contain no spectrally active phytochrome and do not deplete levels of phytochrome A after red-light treatment. High-performance liquid chromatography analyses show that elm1 mutants are unable to convert biliverdin IX alpha to 3Z-phytochromobilin, preventing synthesis of the phytochrome chromophore. Despite the impairment of the phytochrome photoreceptors, elm1 mutants can be grown to maturity in the field. Mature plants retain aspects of the seedling phenotype and flower earlier than wild-type plants under long days. Thus, the elm1 mutant of maize provides the first direct evidence for phytochrome-mediated modulation of flowering time in this agronomically important species.     

广西水稻地方品种耐冷性鉴定及相关分析

对419份广西水稻地方品种初级核心种质进行芽期、苗期的耐冷性鉴定及相关分析,结果表明:广西水稻地方品种芽期、苗期耐冷性主要集中在7级和9级,总体耐冷性较弱。芽期、苗期极强耐冷种质(1级)分别为24份和27份,占参试总数的5.73%和6.44%,其中10份种质芽期和苗期均表现极强耐冷(1级)。芽期、苗期耐冷性呈极显著正相关(r=0.66)。粳稻芽期、苗期耐冷性均显著高于籼稻;粘糯稻之间耐冷性差异是由籼粳稻类型的耐冷差异引起的;来自高寒山区稻作区的品种芽期和苗期平均耐冷表现最强。利用34个SSR标记与芽期、苗期耐冷性进行Pearson相关分析,在第7和第9染色体上,各鉴定出1个同时与芽期和苗期耐冷性相关联的位点。本研究为水稻芽期、苗期耐冷育种提供新的抗源材料,并为水稻耐冷基因定位及机理研究奠定基础。     

Mesocotyl elongation in Digitaria sanguinalis during seedling development

The mesocotyl is an embryonic organ present in Poaceae that plays an important role in seedling emergence. The elongation of this first internode contributes decisively to the coleoptile reaching the soil surface. This study examines the process of mesocotyl elongation under controlled conditions in three caryopsis collection sites of Digitaria sanguinalis (L.) Scop. originating from Spain (Barcelona and Girona) and Argentina that may have two patterns of germination: radicular or coleoptilar. The frequencies of the two germination patterns varied significantly depending on the origin. Light inhibited the elongation of the mesocotyl drastically, resulting in maximum lengths of 3.5 mm, while in darkness the maximum length was 57 mm. The time-course evolution displayed under dark conditions was quite similar for all sites of origin and both germination patterns; the growth rate ranged from 0.23 to 0.30 mm h^? 1. Within localities, caryopses with a coleoptilar pattern of germination showed a lower growth rate than those with a radicular one.     

Seedling vigour and the early growth of transplanted rice (Oryza sativa)

Previous studies suggest that the positive response of transplanted rice (Oryza sativa L.) to nursery fertiliser application was due to increased seedling vigour or possibly to increased nutrient content. This paper presents results of two glasshouse experiments designed to test the hypothesis that seedling vigour was responsible for the response of transplanted seedlings to nursery treatments. The aim of the present study was to explore the concept of seedling vigour of transplanted rice and to determine what plant attributes conferred vigour on the seedlings. Seedling vigour treatments were established by subjecting seedlings to short-term submergence (0, 1 and 2 days/week) in one experiment and to leaf clipping or root pruning and water stress in another to determine their effect on plant growth after transplanting. Submerging seedlings increased plant height but depressed shoot and root dry matter and root:shoot ratio of the seedling at 28 days after sowing. After transplanting these seedlings, prior submergence depressed shoot dry matter at 40 days. Nursery nutrient application increased plant height, increased root and shoot dry matter, but generally decreased root:shoot ratio. Pruning up to 60% of the roots at transplanting decreased shoot and root dry matter, P concentration in leaves at panicle initiation (PI) and straw dry matter and grain yield at maturity. By contrast, pruning 30% of leaves depressed shoot and root dry matter by 30% at PI, and root dry matter and straw and grain yield by 20% at maturity. The combined effects of leaf clipping and root pruning on shoot, root and straw dry matter were largely additive. It is concluded that the response of rice yield to nursery treatments is largely due to increased seedling vigour and can be effected by a range of nutritional as well as non-nutritional treatments of seedlings that increase seedling dry matter, nutrient content, and nutrient concentration. Impairment of leaf growth and to a lesser extent root growth in the nursery depressed seedling vigour after transplanting. However, rather than increasing stress tolerance, seedling vigour was more beneficial when post transplant growth was not limited by nutrient or water stresses.     

水稻萌发耐淹性的遗传分析

水稻(Oryza sativa)萌发耐淹性受到复杂的网络调控, 其分子机制不同于苗期耐淹性的相关机制, 萌发耐淹性的强弱影响着直播稻的成苗率。通过对256份水稻核心种质的萌发耐淹性评估, 发现粳稻和籼稻之间的萌发耐淹性差异并不显著, 都存在广泛的遗传变异。利用以粳稻R0380为供体亲本, 籼稻RP2334为轮回亲本的170个高代回交自交系构建含146个分子标记的连锁图谱, 以低氧胚芽鞘长度为性状指标, 通过复合区间作图法检测到影响萌发耐淹性的4个QTLs(quantitative trait loci), 分别定位于第2(2个)、3(1个)和8号(1个)染色体。贡献率最大的QTL为qGS2.2, 其值为17.34%, 增效等位基因来自轮回亲本籼稻RP2334; 其余3个QTLs的增效等位基因均来自供体亲本粳稻R0380, 贡献率分别为12.86%、9.37%和14.60%。