Predicting individual stem volumes of sugi (Cryptomeria japonica D. Don) plantations in mountainous areas using small-footprint airborne LiDAR

This study investigated which predictor variables with respect to crown properties, derived from small-footprint airborne light detection and ranging (LiDAR) data, together with LiDAR-derived tree height, could be useful in regression models to predict individual stem volumes. Comparisons were also made of the sum of predicted stem volumes for LiDAR-detected trees using the best regression model with field-measured total stem volumes for all trees within stands. The study area was a 48-year-old sugi (Cryptomeria japonica D. Don) plantation in mountainous forest. The topographies of the three stands with different stand characteristics analyzed in this study were steep slope (mean slope ± SD; 37.6° ± 5.8°), gentle slope (15.6° ± 3.7°), and gentle yet rough terrain (16.8° ± 7.8°). In the regression analysis, field-measured stem volumes were regressed against each of the six LiDAR-derived predictor variables with respect to crown properties, such as crown area, volume, and form, together with LiDAR-derived tree height. The model with sunny crown mantle volume (SCV) had the smallest standard error of the estimate obtained from the regression model in each stand. The standard errors (m³) were 0.144, 0.171, and 0.181, corresponding to 23.9%, 21.0%, and 20.6% of the average field-measured stem volume for detected trees in each of these stands, respectively. Furthermore, the sum of the individual stem volumes, predicted by regression models with SCV for the detected trees, occupied 83%–91% of field-measured total stem volumes within each stand, although 69%–86% of the total number of trees were correctly detected by a segmentation procedure using LiDAR data.     

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.     

Chromosomal regions controlling anther culturability in rice (Oryza sativa L.)

Diallel analysis has revealed that anther culturability in rice (Oryza sativa L.) is a quantitative trait controlled by the nuclear genome. Mapping of anther culturability is important to increase the efficiency for green plant regeneration from microspores. In the previous study, we detected distorted segregation of RFLP markers in rice populations derived from the anther culture of an F₁ hybrid between a japonica cultivar ‘Nipponbare’ and an indica cultivar ‘Milyang 23’. To clarify the association between chromosomal regions showing distorted segregation and anther culturability, the anther culturability of doubled haploid lines derived from the same cross combination was examined, and the association between alleles of the RFLP markers, which exhibiting the most distorted segregation on chromosomes 1, 3, 7, 10 and 11, and the anther culturability was evaluated. One region on chromosome 1 was found to control callus formation from microspores, and one region on chromosome 10 appeared to control the ratio of green to albino regenerated plants. In both regions, the Nipponbare allele had positive effects. Three regions on chromosomes 3, 7 and 11, however, showed no significant effect on anther culturability. This revised version was published online in August 2006 with corrections to the Cover Date.     

QTL for spikelet number from a high-yielding rice variety, Hoshiaoba, detected in an introgression line with the genetic background of an indica rice variety, IR64

Total spikelet number per panicle (TSN) is thought to be one of the most important agronomic traits associated with grain production in rice (Oryza sativa L.). We previously reported the development of 334 introgression lines (ILs) with variations in agronomic traits in the genetic background of indica rice variety IR64. Among these, an IL derived from high-yielding rice variety Hoshiaoba showed significantly higher TSN than IR64. We therefore have conducted a quantitative trait locus (QTL) analysis for TSN in an F₂ population of IL × IR64 to ascertain the genetic basis for the high TSN of the IL. The analysis revealed the presence of a QTL for TSN on chromosome 7, where several QTLs for grain number have been previously reported. We developed a near-isogenic line (NIL) for this QTL by using DNA marker-assisted selection and characterized its effect. The NIL showed significantly higher TSN than IR64. These results suggest that the QTL and the NIL will be useful materials in breeding programs aimed at increasing TSN.     

QTLs for phosphorus deficiency tolerance detected in upland NERICA varieties

Phosphorous (P) deficiency is a major yield limiting factor in rice (Oryza sativa L.) production. The interspecific New Rice for Africa (NERICA) varieties combine general stress tolerance from African cultivated rice (Oryza glaberrima Steud) with characteristics associated with high yield from O. sativa. However, little is known about their ability to tolerate P deficiency. Here, we examined the variation for tolerance to P deficiency among the 18 upland NERICAs and their parents in multi‐year field experiments. The good performance under P deficiency of the O. glaberrima parent CG 14 and some NERICAs suggested that these tolerant NERICAs contain loci associated with P deficiency tolerance inherited from CG 14. Additionally, four QTL clusters for P deficiency tolerance were detected on chromosomes 4, 6 and 11 using F₃ lines derived from the cross between the P deficiency tolerant variety NERICA10 and a Japonica‐type sensitive variety ‘Hitomebore’. These QTLs represent the first step in identifying stress tolerance genes from O. glaberrima that could subsequently be used to enhance P deficiency tolerance in O. sativa.     

Genotypic variation in grain phosphorus concentration,and opportunities to improve P-use efficiency in rice

Continual removal of phosphorus (P) from fields in rice grains at harvest results in lower soil fertility in low-input farming systems and drives the need for fertiliser inputs in high-input farming systems. High-P content in rice grains (the majority as phytate) contributes little to human nutrition and agronomic practices such as growing seedlings in high-P media or seed P coating at sowing (in direct-sown crops) may overcome the reported need for high-P seed for seedling establishment. Thus, reducing the amount of P in rice grains at maturity through breeding may represent a novel means to reduce ‘mining’ of soil P. We investigated the uptake and partitioning of P in rice plants and examined the scope for breeding rice with lower grain P by assessing genotypic variation for phosphorus harvest index (PHI) and seed P concentrations among a set of 38 rice genotypes in the field. At maturity approximately 75% of total plant P was found in grains and translocation of P from stems and leaves contributed substantially to grain P. However, unlike other cereals such as wheat, rice plants continued dry matter and P accumulation until maturity with approximately 40% of total plant P taken up post anthesis. In the field study, PHI differed significantly among genotypes (from 57 to 87) but was highly correlated to HI (P ≤ 0.001), suggesting that exploiting genotypic variation for this trait may be counterproductive. Grain P concentrations varied from 1.96 to 3.18 mg P g⁻¹, and were neither associated with reductions in grain yield or seed size, nor significantly correlated to HI. Grain P concentration therefore appears to be a suitable screening criterion and the 50% variation observed among genotypes suggests that scope exists for breeding rice with lower grain P concentration to reduce the off-take of P from rice fields at harvest.     

QTL analysis for soil‐surface roots originating from a New Plant Type rice (Oryza sativa L.)

The introgression line YTH16 harbouring chromosome segments from the New Plant Type cultivar IR65600–87–2‐2–3 with genetic background of an Indica Group rice IR 64 forms soil‐surface roots. To clarify the genetic mechanism, QTL analysis was performed using hybrid populations derived from a cross between IR 64 and YTH16. A total of eight QTLs were detected in the three introgressed segments on chromosomes 2, 5 and 7. Seven chromosome segment lines (CSLs) combining these three QTL regions were selected from the progenies. The two CSLs harbouring a single region (excluding the CSL with a region on chromosome 5) showed high scores and low means of root angle distribution in comparison with IR 64. Four CSLs harbouring two or three regions showed high scores and low means of root angle distribution in comparison with YTH16 and the CSLs harbouring a single QTL region. These results indicated that the soil‐surface rooting of YTH16 was controlled by the three QTLs’ regions and that chr. 5 particularly played a role in supporting the effect with others.     

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

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