Qinglu Zhang

Characterization of the main effects, epistatic effects and their environmental interactions of QTLs on the genetic basis of yield traits in rice

Abstract.Main effects, epistatic effects and their environmental interactions of QTLs are all important genetic components of quantitative traits. In this study, we analyzed the main effects, epistatic effects of the QTLs, and QTL by environment interactions (QEs) underlying four yield traits, using a population of 240 recombinant inbred lines from a cross between two rice varieties tested in replicated field trials. A genetic linkage map with 220 DNA marker loci was constructed. A mixed linear model approach was used to detect QTLs with main effects, QTLs involved in digenic interactions and QEs. In total, 29 QTLs of main effects, and 35 digenic interactions involving 58 loci were detected for the four traits. Thirteen QTLs with main effects showed QEs; no QE was detected for the QTLs involved in epistatic interactions. The amount of variations explained by the QTLs of main effect were larger than the QTLs involved in epistatic interactions, which in turn were larger than QEs for all four traits. This study illustrates the ability of the analysis to assess the genetic components underlying the quantitative traits, and demonstrates the relative importance of the various components as the genetic basis of yield traits in this population.

Identification and mapping of two brown planthopper resistance genes in rice

Abstract The brown planthopper (BPH) is one of the most serious insect pests of rice. In this study, we conducted a molecular marker-based genetic analysis of the BPH resistance of ’B5’, a highly resistant line that derived its resistant genes from the wild rice Oryza officinalis. Insect resistance was evaluated using 250 F3 families from a cross between ’B5’ and ’Minghui 63’, based on which the resistance of each F2 plant was inferred. Two bulks were made by mixing, respectively, DNA samples from highly resistant plants and highly susceptible plants selected from the F2 population. The bulks were surveyed for restriction fragment length polymorphism using probes representing all 12 chromosomes at regular intervals. The survey revealed two genomic regions on chromosome 3 and chromosome 4 respectively that contained genes for BPH resistance. The existence of the two loci were further assessed by QTL (quantitative trait locus) analysis, which resolved these two loci to a 14.3-cM interval on chromosome 3 and a 0.4-cM interval on chromosome 4. Comparison of the chromosomal locations and reactions to BPH biotypes indicated that these two genes are different from at least nine of the ten previously identified BPH resistance genes. Both of the genes had large effects on BPH resistance and the two loci acted essentially independent of each other in determining t he resistance. These two genes may be a useful BPH resistance resource for rice breeding programs.

Molecular dissection of seedling-vigor and associated physiological traits in rice.

Abstract.seedling-vigor is important for crop establishment. There have been reported quantitative trait locus (QTL) analyses on seedling-vigor related morphological traits. However, physiological understanding of these detected QTLs is rather limited. In this study, we employed a recombinant inbred population to detect QTLs for seedling-vigor traits and physiological traits related to seedling-vigor. Germination rate and seedling growth were measured to quantify seedling-vigor. Total amylase activity, α-amylase activity, reducing sugar content, root activity and seed weight were determined. Correlations were observed between the seedling-vigor and physiological traits. QTL analysis reveals that the intervals of RG393-C1087-RZ403 on chromosome 3, C246-RM26-C1447 and R830-R3166-RG360-C734b on chromosome 5, and the interval of Waxy on chromosome 6 are the four main chromosomal regions controlling seedling-vigor. Several QTLs for amylase activities, reducing sugar content and root activity were localized in the similar regions as the QTLs for seedling-vigor. The results suggest that these traits were under the control of pleiotropic and/or closely linked QTLs. The implications of the results in the understanding of the physiological basis of seedling-vigor were discussed.

Pyramiding and evaluation of three dominant brown planthopper resistance genes in the elite indica rice 9311 and its hybrids

BACKGROUND Brown planthopper (BPH), Nilaparvata lugens Stål, is the most devastating insect pest in rice-producing areas. Three dominant BPH resistance genes (Bph14, Bph15, Bph18) were pyramided into elite indica rice 9311 and its hybrids using marker-assisted selection. Gene effectiveness was evaluated on the basis of seedling and adult rice resistance, honeydew weight and survival rate of BPH. RESULTS All three genes affected BPH growth and development and antibiotic factors, resulting in both seedling and adult resistance. Bph15 had the greatest effect on conferring resistance to BPH. The results showed an additive effect of pyramiding genes, the order of the gene effect being 14/15/18 ≥ 14/15 > 15/18 ≥ 15 > 14/18 ≥ 14 ≥ 18 > none. The pyramided or single-gene introgression hybrids showed greater resistance than conventional hybrids, although the heterozygous genotypes had weaker effects than the corresponding homozygous genotypes. Furthermore, field trial data demonstrated that yields of improved 9311 lines were higher than or similar to that of the control under natural field conditions. These improved versions can be immediately used in hybrid improvement and production. CONCLUSION Compared with controls, pyramided lines and hybrids with three genes showed the strongest resistance to BPH, without a yield decrease.

OsAAP6 functions as an important regulator of grain protein content and nutritional quality in rice

Grains from cereals contribute an important source of protein to human food, and grain protein content (GPC) is an important determinant of nutritional quality in cereals. Here we show that the quantitative trait locus (QTL) qPC1 in rice controls GPC by regulating the synthesis and accumulation of glutelins, prolamins, globulins, albumins and starch. qPC1 encodes a putative amino acid transporter OsAAP6, which functions as a positive regulator of GPC in rice, such that higher expression of OsAAP6 is correlated with higher GPC. OsAAP6 greatly enhances root absorption of a range of amino acids and has effects on the distribution of various amino acids. Two common variations in the potential cis-regulatory elements of the OsAAP6 5′-untranslated region seem to be associated with GPC diversity mainly in indica cultivars. Our results represent the first step toward unravelling the mechanism of regulation underlying natural variation of GPC in rice.

Improving blast resistance of Jin 23B and its hybrid rice by marker-assisted gene pyramiding

Rice blast is one of the most serious diseases in rice (Oryza sativa L.) worldwide. Jin 23B is the maintainer line, a parent for a number of hybrid rice varieties used widely in China. However, Jin 23B is highly susceptible to rice blast. In this study, Pi1, Pi2, and D12 were introgressed to improve the blast resistance of Jin 23B and its derived hybrids, Jinyou 402 and Jinyou 207, by marker-assisted selection (MAS). The improved Jin 23B, which carried single, two, and three genes, were evaluated for their resistance to rice blast using natural inoculation methods in disease nursery of Xianfeng, Hubei, China. The results showed that, the greater the number of genes contained in the improved Jin 23B and hybrids, the higher the resistance to rice blast. Pi1, Pi2, and D12 showed a strong dosage effect on the resistance to blast in the hybrid background during the entire growth duration in the field condition, being very useful for breeding blast-resistant hybrids. The result of examining agronomic traits showed that the improved Jin 23B and its derived hybrid rice were taller than or similar to controls, when there was no disease stress.

Genetic bases of instability of male sterility and fertility reversibility in photoperiod-sensitive genic male-sterile rice

Abstract Photoperiod-sensitive genetic male-sterile (PSGMS) rice, with its male fertility regulated by photoperiod length, is very useful for hybrid rice development. However, breeding for new PSGMS lines has faced two major difficulties – the stability of male sterility and the reversibility of male fertility. In this study we assessed the genetic bases of stability of sterility and fertility reversibility using a molecular marker-based approach. A cross was made between two newly bred PSGMS lines: Peiai 64S, which has a stable sterility but is difficult to reverse to fertility, and 8902S, which has a unstable sterility but is easy to reverse to fertility. The fertility of the parents and of the F1 and F2 populations was repeatedly examined under 11 different long-day and short-day conditions. The genetic effects were assayed by interval mapping and two-way analyses of variance using the F2 data of 128 polymorphic loci representing all the 12 rice chromosomes. The analyses resolved a number of single-locus QTLs and two-locus interactions under both long-day and short day conditions. The interactions involved a large number of loci, most of which were not detectable on a single-locus basis. The results showed that the genetic bases of both stability of sterility and reversibility of fertility are the joint effects of the additive effects of the QTLs and additive-by-additive components of two-locus interactions. The implications of these findings in hybrid rice development are also discussed.

A new finely mapped Oryza australiensis-derived QTL in rice confers resistance to brown planthopper

Brown planthopper (BPH) is the most destructive pest of rice in Asia. The BPH resistance in the introgression line IR65482-17-511-5-7 (IR65482-17) is derived from the wild rice species Oryza australiensis. An F2:3 population from a cross between Zhenshan 97 (ZS97) and IR65482-17 was used to map three quantitative trait loci (QTLs) for seedling resistance and feeding rate to BPH. The loci were distributed on chromosomes 2, 4 and 12. The QTL qBph4.2 on chromosome 4 had the largest effect, and contributed 36-44% of the phenotypic variance with a LOD score of 19-29. To validate the effect of qBph4.2, two near-isogenic lines (NILs) containing the qBph4.2 locus in the backgrounds of ZS97 and 9311 were developed by marker-assisted backcrossing (MABC). BPH bioassays showed that lines homozygous for the IR65482-17 allele (NIL+) of qBph4.2 tented to have significantly higher seedling resistance to BPH than those homozygous for the ZS97 or 9311 alleles (NIL-). Resistance was associated with a lower feeding rate by the insect. qBph4.2 was delimited to a ~300 kb (0.04 cM) region flanked by markers RM261 and S1, and co-segregating with XC4-27. This study will facilitate map-based cloning and marker-assisted selection of the gene, and permits further studies of gene function and resistance mechanisms in rice: BPH interaction.

QTL analysis on rice grain appearance quality, as exemplifying the typical events of transgenic or backcrossing breeding

Rice grain shape and yield are usually controlled by multiple quantitative trait loci (QTL). This study used a set of F9–10 recombinant inbred lines (RILs) derived from a cross of Huahui 3 (Bt/Xa21) and Zhongguoxiangdao, and detected 27 QTLs on ten rice chromosomes. Among them, twelve QTLs responsive for grain shape/ or yield were mostly reproducibly detected and had not yet been reported before. Interestingly, the two known genes involved in the materials, with one insect-resistant Bt gene, and the other disease-resistant Xa21 gene, were found to closely link the QTLs responsive for grain shape and weight. The Bt fragment insertion was firstly mapped on the chromosome 10 in Huahui 3 and may disrupt grain-related QTLs resulting in weaker yield performance in transgenic plants. The introgression of Xa21 gene by backcrossing from donor material into receptor Minghui 63 may also contain a donor linkage drag which included minor-effect QTL alleles positively affecting grain shape and yield. The QTL analysis on rice grain appearance quality exemplified the typical events of transgenic or backcrossing breeding. The QTL findings in this study will in the future facilitate the gene isolation and breeding application for improvement of rice grain shape and yield.

Development and evaluation of near-isogenic lines for brown planthopper resistance in rice cv. 9311

Brown planthopper (BPH) is the most destructive pest of rice in Asia. To date 29 BPH resistance genes have been identified, but only a few genes are being used in breeding due to inefficient markers for marker-assisted selection (MAS) and little knowledge of the real effects of the genes. In this study we individually transferred 13 genes or QTLs (Bph14, QBph3, QBph4, Bph17, Bph15, Bph20, Bph24, Bph6, Bph3, Bph9, Bph10, Bph18 and Bph21) into cultivar 9311 by marker assisted backcross breeding (MABB). Through positive and negative selection we narrowed the segments from donors containing Bph14, Bph15, Bph6 and Bph9 to 100–400 kb. Whole-genome background selection based on a high resolution SNP array was performed to maximize reconstitution of the recurrent parent genome (RPG 99.2–99.9%). All genes reduced BPH growth and development and showed antibiotic responses in seedlings. Based on genetic effects and amino acid sequences of genes in three clusters we inferred that Bph10 and Bph21 might be identical to Bph26, whereas Bph9 and Bph18 were different. Bph15 might be same with Bph17, but QBph4, Bph20 and Bph24 might be different. We believe that these NILs will be useful in rice BPH resistance research and breeding.