QTL mapping for nitrogen-use efficiency and nitrogen-deficiency tolerance traits in rice

Plant and Soil - The improvement of nitrogen-deficiency tolerance (NDT) and nitrogen-use efficiency (NUE) traits is an important objective of many rice breeding programs. A better understanding of...     

Freezing tolerance of citrus, spinach, and petunia leaf tissue : osmotic adjustment and sensitivity to freeze induced cellular dehydration

Seasonal variations in freezing tolerance, water content, water and osmotic potential, and levels of soluble sugars of leaves of field-grown Valencia orange (Citrus sinensis) trees were studied to determine the ability of citrus trees to cold acclimate under natural conditions. Controlled environmental studies of young potted citrus trees, spinach (Spinacia pleracea), and petunia (Petunia hybrids) were carried out to study the water relations during cold acclimation under less variable conditions. During the coolest weeks of the winter, leaf water content and osmotic potential of field-grown trees decreased about 20 to 25%, while soluble sugars increased by 100%. At the same time, freezing tolerance increased from lethal temperature for 50% (LT₅₀) of −2.8 to −3.8°C. In contrast, citrus leaves cold acclimated at a constant 10°C in growth chambers were freezing tolerant to about −6°C. The calculated freezing induced cellular dehydration at the LT₅₀ remained relatively constant for field-grown leaves throughout the year, but increased for leaves of plants cold acclimated at 10°C in a controlled environment. Spinach leaves cold acclimated at 5°C tolerated increased cellular dehydration compared to nonacclimated leaves. Cold acclimated petunia leaves increased in freezing tolerance by decreasing osmotic potential, but had no capacity to change cellular dehydration sensitivity. The result suggest that two cold acclimation mechanisms are involved in both citrus and spinach leaves and only one in petunia leaves. The common mechanism in all three species tested was a minor increase in tolerance (about −1°C) resulting from low temperature induced osmotic adjustment, and the second in citrus and spinach was a noncolligative mechanism that increased the cellular resistance to freeze hydration.     

Mapping osmotic adjustment in an advanced back-cross inbred population of rice

Osmotic adjustment is one of several characters putatively associated with drought tolerance in rice. Indica cultivars are known to have a greater capacity for osmotic adjustment than japonica cultivars. We developed an advanced back-cross population using an indica donor, IR62266-42-6-2, to introgress osmotic adjustment into an elite japonica cultivar, IR60080-46A. One hundred and fifty BC₃F₃ families were genotyped using microsatellites and RFLP markers, and a few candidate genes. We evaluated osmotic adjustment in these lines under greenhouse conditions using the re-hydration technique. Using the composite interval mapping technique, we detected 14 QTLs located on chromosomes 1, 2, 3, 4, 5, 7, 8 and 10 that together explained 58% of the phenotypic variability. Most, but not all, of the alleles with positive effects came from the donor parent. On chromosome 8, two QTLs were associated in repulsion. The QTL locations were in good agreement with previous studies on this trait on rice and in other cereals. Some BC₃F₃ lines carried the favorable alleles at the two markers flanking up to four QTLs. Intercrossing these lines followed by marker-aided selection in their progenies will be necessary to recover lines with levels of osmotic adjustment equal to the donor parent. The advanced back-cross strategy appeared to be an appropriate method to accelerate the process of introgressing interesting traits into elite material.Communicated by Q. Zhang     

Contribution of osmotic adjustment to the dehydration tolerance of water-stressed pigeon pea (Cajanus cajan (L.) millsp.) leaves

Abstract Water-stressed pigeonpea leaves have high levels of osmotic adjustment at low leaf water potentials. The possible contribution of this adjustment of dehydration tolerance of leaves was examined in plants grown in a controlled environment. Osmotic adjustment was varied by withholding water from plants growing in differing amounts of soil, which resulted in different rates of decline of leaf water potential. The level of osmotic adjustment was inversely related to leaf water potential in all treatments. In addition, at any particular water potential, plants that had experienced a rapid development of stress exhibited less osmotic adjustment than plants that experienced a slower development of stress. Leaves with different levels of osmotic adjustment died at water potentials between –3.4 and –6.3 MPa, but all leaves died at a similar relative water content (32%). Consequently, leaves died when relative water content reached a lethal value, rather than when a lethal leaf water potential was reached. Osmotic adjustment delayed the time and lowered the leaf water potential when the lethal relative water content occurred, because it helped maintain higher relative water contents at low leaf water potentials. The consequences of osmotic adjustment for leaf survival in water-stressed pigeonpea are discussed.     

Contribution of inorganic components to osmotic adjustment and leaf folding for drought tolerance in pearl millet

Pearl millet, Pennisetum glaucum , is capable of adapting to severely dry environmental conditions. In order to elucidate the mechanism of adaptation to highly dehydrated conditions, we selected both tolerant (IP8210) and susceptible (IP8949) accessions from a total of 15 pearl millet accessions and characterized their morphological and physiological responses to severe drought stress. When these selected accessions were stressed with a severe drought treatment, the leaves of IP8210 exhibited upright folding, a response that effectively reduces the evaporative surface area of the canopy. On the contrary, the leaves of IP8949 exhibited wilting and did not appear to adapt to the drought stress. In comparison with IP8949, the capacity of osmotic adjustment (OA) was greater in both younger leaves and stems of IP8210, while their decrease in relative water content was different. IP8210 accumulated higher concentrations of NO₃^– than IP8949 in response to drought stress. In addition to inorganic solutes, several organic components such as sucrose, glucose, quaternary ammonium compounds, and amino acids including proline were also accumulated. IP8210 tended to accumulate more amino acids, typically due to the accumulation of asparagine and proline, while IP8949 accumulated more soluble sugars. While it is possible that K⁺ and NO₃^– were the major components contributing to osmotic regulations, sugars and amino acids might also function as a cytoprotectant, in addition to their role as osmoprotectants. Collectively, these results demonstrate that the morphological adaptation of leaf folding, OA in both the younger leaves and the stem, and the accumulation of NO₃^– and amino acids during earlier stress period contribute to superior drought tolerance that was exhibited in IP8210 of pearl millet.     

QTL: their place in engineering tolerance of rice to salinity

Secondary salinization and its relationship to irrigation are strong incentives to improve the tolerance of crops to salinity and to drought. Achieving this through the pyramiding of physiological traits (phenotypic selection without knowledge of genotype) is feasible. However, wide application of this approach is limited by the practicalities of assessing not only the parents, but also large numbers of individuals and families in segregating generations. Genotypic information is required in the form of markers for any quantitative trait loci involved (marker-assisted selection) or of direct knowledge of the genes. In the absence of adequate candidate genes for salt tolerance, a quantitative trait locus/marker-assisted selection approach has been used here. Putative markers for ion transport and selectivity, identified from analysis of amplified fragment length polymorphism, had been discovered within a custom-made mapping population of rice. Here it is reported that none of these markers showed any association with similar traits in a closely related population of recombinant inbred lines or in selections of a cultivar. Whilst markers will be of value in using élite lines from the mapping population in backcrossing, this has to be considered alongside the effort required to develop and map any given population. This result cautions against any expectation of a general applicability of markers for physiological traits. It is concluded that direct knowledge of the genes involved is needed. This cannot be achieved at present by positional cloning. The elucidation of candidate genes is required. Here the problem lies not in the analysis of gene expression but in devising protocols in which only those genes of interest are differentially affected by the experimental treatments.     

Saturation mapping of QTL regions and identification of putative candidate genes for drought tolerance in rice

We have developed 85 new markers (50 RFLPs, 5 SSRs, 12 DD cDNAs, 9 ESTs, 8 HSP-encoding cDNAs and one BSA-derived AFLP marker) for saturation mapping of QTL regions for drought tolerance in rice, in our efforts to identify putative candidate genes. Thirteen of the markers were localized in the close vicinity of the targeted QTL regions. Fifteen of the additional markers mapped, respectively, inside one QTL region controlling osmotic adjustment on chromosome 3 ( oa3.1) and 14 regions that affect root traits on chromosomes 1, 2, 4, 5, 6, 7, 8, 9, 10 and 12. Differential display was used to identify more putative candidate genes and to saturate the QTL regions of the genetic map. Eleven of the isolated cDNA clones were found to be derived from drought-inducible genes. Two of them were unique and did not match any genes in the GenBank, while nine were highly similar to cDNAs encoding known proteins, including a DnaJ-related protein, a zinc-finger protein, a protease inhibitor, a glutathione-S-transferase, a DNA recombinase, and a protease. Twelve new cDNA fragments were mapped onto the genetic linkage map; seven of these mapped inside, or in close proximity to, the targeted QTL regions determining root thickness and osmotic adjustment capacity. The gene I12A1, which codes for a UDP-glucose 4-epimerase homolog, was identified as a putative target gene within the prt7.1/brt7.1 QTL region, as it is involved in the cell wall biogenesis pathway and hence may be implicated in modulating the ability of rice roots to penetrate further into the substratum when exposed to drought conditions. RNAs encoding elongation factor 1, a DnaJ-related protein, and a homolog of wheat zinc-finger protein were more prominently induced in the leaves of IR62266 (the lowland rice parent of the mapping materials used) than in those of CT9993 (the upland rice parent) under drought conditions. Homologs of 18S ribosomal RNA, and mRNAs for a multiple-stress induced zinc-finger protein, a protease inhibitor, and a glutathione-S-transferase were expressed at significantly higher levels in CT9993 than in IR62266. Thus several genes involved in the regulation of DNA structure and mRNA translation were found to be drought-regulated, and may be implicated in drought resistance.Communicated by R. Hagemann     

Combining drought and submergence tolerance in rice: marker-assisted breeding and QTL combination effects

TDK1 is a popular rice variety from the Lao PDR. Originally developed for irrigated conditions, this variety suffers a high decline in yield under drought conditions. Studies have identified three quantitative trait loci (QTLs) for grain yield under drought conditions, qDTY _3.1 , qDTY _6.1 , and qDTY _6.2 , that show a high effect in the background of this variety. We report here the pyramiding of these three QTLs with SUB1 that provides 2–3 weeks of tolerance to complete submergence, with the aim to develop drought- and submergence-tolerant near-isogenic lines (NILs) of TDK1. We used a tandem approach that combined marker-assisted backcross breeding with phenotypic selection to develop NILs with high yield under drought stress and non-stress conditions and preferred grain quality. The effect of different QTL combinations on yield and yield-related traits under drought stress and non-stress conditions is also reported. Our results show qDTY _3.1 to be the largest and most consistent QTL affecting yield under drought conditions, followed by qDTY _6.1 and qDTY _6.2 , respectively. QTL class analysis also showed that lines with a combination of qDTY _3.1 and qDTY _6.1 consistently showed a higher tolerance to drought than those in which one of these QTLs was missing. In countries such as Lao PDR, where large areas under rice cultivation suffer vegetative-stage submergence and reproductive-stage drought, these lines could ensure yield stability. These lines can also serve as valuable genetic material to be used for further breeding of high-yielding, drought- and submergence-tolerant varieties in local breeding programs.     

QTL mapping in rice

In the past 10 years, interest in applying the tools of molecular genetics to the problem of increasing world rice production has resulted in the generation of two highly saturated, molecular linkage maps of rice, and the localization of numerous genes and quantitative trait loci (QTLs). Primary studies have identified QTLs associated with disease resistance, abiotic stress tolerance and yield potential of rice in a range of ecosystems. The ability to identify, manipulate and potentially clone individual genes involved in quantitatively inherited characters, combined with the demonstrated conservation of numerous linkage blocks among members of the grass family, emphasizes the contribution of map-based genetic analyses both to applied and to basic crop research.     

籼稻稻米碾磨与外观品质性状的QTL定位

文章利用籼籼交组合特青/IRBB衍生的重组自交系群体, 在2个环境下对稻米碾磨品质和外观品质进行QTL定位。共计检测到控制稻米碾磨品质的QTL 12个和控制外观品质的QTL 18个, 包括糙米率8个、精米率2个、整精米率2个、粒长7个、粒宽5个和长宽比6个, 这些QTL分布于除第4和12染色体外的其他10条染色体上。其中, 第3染色体涵盖粒形基因GS3的区域对粒长、长宽比、糙米率和整精米率具有较大效应, 其献率分别为56.71%、42.23%、10.05%和4.91%; 第5染色体涵盖粒宽基因GW5的区域对粒宽、长宽比、糙米率和精米率具有较大效应, 表型变异贡献率分别为59.51%、36.68%、19.51%和4.56%。此外, 第6染色体涵盖直链淀粉含量基因Wx的区域对糙米率和精米率具有较小效应。GS3和GW5对糙米率和粒形具有重要作用。     

Fine mapping of the qCTS12 locus, a major QTL for seedling cold tolerance in rice

The temperate japonica rice cultivar M202 is the predominant variety grown in California due to its tolerance to low temperature stress, good grain quality and high yield. Earlier analysis of a recombinant inbred line mapping population derived from a cross between M202 and IR50, an indica cultivar that is highly sensitive to cold stress, resulted in the identification of a number of QTL conferring tolerance to cold-induced wilting and necrosis. A major QTL, qCTS12, located on the short arm of chromosome 12, contributes over 40% of the phenotypic variance. To identify the gene(s) underlying qCTS12, we have undertaken the fine mapping of this locus. Saturating the short arm of chromosome 12 with microsatellite markers revealed that qCTS12 is closest to RM7003. Using RM5746 and RM3103, which are immediately outside of RM7003, we screened 1,954 F₅-F₁₀ lines to find recombinants in the qCTS12 region. Additional microsatellite markers were identified from publicly available genomic sequence and used to fine map qCTS12 to a region of approximately 87 kb located on the BAC clone OSJNBb0071I17. This region contains ten open reading frames (ORFs) consisting of five hypothetical and expressed proteins of unknown function, a transposon protein, a putative NBS-LRR disease resistance protein, two zeta class glutathione S-transferases (OsGSTZ1 and OsGSTZ2), and a DAHP synthetase. Further fine mapping with markers developed from the ORFs delimited the QTL to a region of about 55 kb. The most likely candidates for the gene(s) underlying qCTS12 are OsGSTZ1 and OsGSTZ2.The mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture.     

Salt tolerance of Beta macrocarpa is associated with efficient osmotic adjustment and increased apoplastic water content

The chenopod Beta macrocarpa Guss (wild Swiss chard) is known for its salt tolerance, but the mechanisms involved are still debated. In order to elucidate the processes involved, we grew wild Swiss chard exposed to three salinity levels (0, 100 and 200 mm NaCl) for 45 days, and determined several physiological parameters at the end of this time. All plants survived despite reductions in growth, photosynthesis and stomatal conductance in plants exposed to salinity (100 and 200 mm NaCl). As expected, the negative effects of salinity were more pronounced at 200 mm than at 100 mm NaCl: (i) leaf apoplastic water content was maintained or increased despite a significant reduction in leaf water potential, revealing the halophytic character of B. macrocarpa; (ii) osmotic adjustment occurred, which presumably enhanced the driving force for water extraction from soil, and avoided toxic build up of Na⁺ and Cl^– in the mesophyll apoplast of leaves. Osmotic adjustment mainly occurred through accumulation of inorganic ions and to a lesser extent soluble sugars; proline was not implicated in osmotic adjustment. Overall, two important mechanisms of salt tolerance in B. macrocarpa were identified: osmotic and apoplastic water adjustment.     

A relationship between tolerance to dehydration of rice cell lines and ability for ABA synthesis under stress.

Plant dehydration is commonly caused by some adverse environmental conditions such as salinity, drought and freezing. As the plant hormone abscisic acid (ABA) is involved in responses to water stress, we studied its putative relationship with the degree of tolerance to these abiotic stresses. For this purpose we used cell lines that had been established from mature embryos of rice (Oryza sativa L, cvs. Bahia and Bomba), and selected by their high (L-T) or low (L-S) levels of tolerance to each type of stress. Tolerance of rice calli to either osmotic, saline, or freezing stress was generally improved by a previous treatment with ABA. This ABA effect was evident in those callus lines with low tolerance (L-S), as their ability to recover from stress increased up to three fold. Independent of the cultivar used, there were no significant differences in the endogenous ABA contents between untreated L-T and L-S lines. However, upon stress, the increase in endogenous ABA was higher in L-T than in L-S lines. These results, together with those obtained by using Fluridone, an inhibitor of ABA synthesis, show that differences in the level of cell tolerance to osmotic, saline and freezing stress are related to their different capacity of ABA synthesis under stress conditions.     

Multiphasic osmotic adjustment in a euryhaline cyanobacterium

Abstract Transfer of Synechocystis PCC6714 from a freshwater medium to a saline medium caused the cells to shrink; rapid entry of NaCl resulted in a partial recovery of cellular volume within 2 min. Active extrusion of internal Na⁺ in exchange for extracellular K⁺ then occurred (within 20 min). Finally, the low- M _r carbohydrates sucrose and glucosylglycerol were accumulated and internal KC1 levels declined. In long-term growth experiments, the relative importance of sucrose as a component of the low- M _r organic solute fraction decreased and glucosylglycerol became the single most important intracellular solute. These observations demonstrate that several inorganic and organic solutes are involved in osmotic adjustment in this cyanobacterium, with sequential changes in the relative importance of each solute following transfer to a saline medium.     

QTL mapping and confirmation for tolerance of anaerobic conditions during germination derived from the rice landrace Ma-Zhan Red

Wide adoption of direct-seeded rice practices has been hindered by poorly leveled fields, heavy rainfall and poor drainage, which cause accumulation of water in the fields shortly after sowing, leading to poor crop establishment. This is due to the inability of most rice varieties to germinate and reach the water surface under complete submergence. Hence, tolerance of anaerobic conditions during germination is an essential trait for direct-seeded rice cultivation in both rainfed and irrigated ecosystems. A QTL study was conducted to unravel the genetic basis of tolerance of anaerobic conditions during germination using a population derived from a cross between IR42, a susceptible variety, and Ma-Zhan Red, a tolerant landrace from China. Phenotypic data was collected based on the survival rates of the seedlings at 21 days after sowing of dry seeds under 10 cm of water. QTL analysis of the mapping population consisting of 175 F_2:3 families genotyped with 118 SSR markers identified six significant QTLs on chromosomes 2, 5, 6, and 7, and in all cases the tolerant alleles were contributed by Ma-Zhan Red. The largest QTL on chromosome 7, having a LOD score of 14.5 and an R ² of 31.7 %, was confirmed using a BC₂F₃ population. The QTLs detected in this study provide promising targets for further genetic characterization and for use in marker-assisted selection to rapidly develop varieties with improved tolerance to anaerobic condition during germination. Ultimately, this trait can be combined with other abiotic stress tolerance QTLs to provide resilient varieties for direct-seeded systems.     

In vitro screening procedure for osmotic tolerance in Prunus

Significant growth differences (p<0.01) were observed for two micropropagated Prunus accessions after 14 days in culture when 685 mM mannitol was included in Quoirin and Lepoivre nutrient medium. While there was an 11% growth increase in fresh weight during the 28-day culture period for accession K537-067, explants from New Jersey Plumcot No. 3 increased fresh weight an average of 123%. Similar tests were conducted to determine the repeatability of this short term in vitro screening procedure. Explants of Mananna 2624 were subjected to two levels of mannitol, 275 mM and 550 mM, included in the Quoirin and Lepoivre nutrient medium. Three successive 28-day tests were conducted. Explants were examined at both 14 and 28 days after the onset of the experiment for net growth changes. Addition of mannitol to the nutrient medium at concentrations of 275 mM and 550 mM decreased explant fresh weights of Marianna 2624 to 36% and 28% of controls, respectively, at 28 days past initial culture. Initial fresh weight and fresh weight changes at day 14 were significantly different (p 0.05) between tests. No significant differences existed between tests with regard to weight changes at 28 days past initial culture. This information may aid Prunus breeders in the choice of procedures for inducing drought stress and screening large numbers of plant accessions.Abbreviations K5 K537-067 - M2624 Marianna 2624 - NJPC3 New Jersey Plumcot No. 3 - Q & L Quoirin and Lepoivre     

Cold tolerance and dehydration in Enchytraeidae from Svalbard

When cooled in contact with moisture, eight species of arctic Enchytraeidae from Svalbard were killed by freezing within minutes or hours at −3 and −5 °C; an exception was Enchytraeus kincaidi which survived for up to 2 days. When the temperature approached 0 °C the enchytraeids apparently tried to escape from the moist soil. The supercooling capacity of the enchytraeids was relatively low, with mean supercooling points of −5 to −8 °C. In contrast, specimens of several species were extracted from soil cores that had been frozen in their intact state at −15 °C for up to 71 days. Compared to freezing in a moist environment, higher survival rates were obtained during cooling at freezing temperatures in dry soil. Survival was recorded in species kept at −3 °C for up to 35 days, and in some species kept at −6 °C for up to 17 days. Slow warming greatly increased survival rates at −6 °C . The results strongly suggest that arctic enchytraeids avoid freezing by dehydration at subzero temperatures. In agreement with this, weight losses of up to ca. 42% of fresh weight were recorded in Mesenchytraeus spp. and of up to 55% in Enchytraeus kincaidi at water vapour pressures above ice at −3 to −6 °C. All specimens survived dehydration under these conditions. Accepted: 12 December 1997     

QTL pyramiding for producing nutritious and safe rice grains

正Breeding of rice varieties that are enriched with essential micronutrients and simultaneously have reduced levels of toxic elements in grains is largely unexplored in rice breeding practice. In this issue of JIPB, Liu et al.(2020)developed two rice lines with a low level of cadmium and simultaneously high levels of zinc or selenium accumulation in the grains, thus providing elite genetic materials for breeding rice varieties that are important for addressing mineral malnutrition and ensuring food safety.m entary