Genetic analysis and QTL mapping for grain chalkiness characteristics of brown rice (Oryza sativa L.)

Grain chalkiness is one of the important appearance qualities in rice marketing. But it is a complex trait, controlled by polygenes and easily influenced by the environment. Genetic analysis and QTL detection was carried out on six characteristics of grain chalkiness consisting of the percentage of chalkiness (PGC), white belly (PWB) and white core grains (PWC), and the area of chalkiness (CA), white belly (WBA) and white core (WCA) in brown rice. A total of 16 main-effect QTLs associated with chalkiness characteristics of brown rice were mapped on seven chromosomes over two years. Among them,qPGC7.1 andqPWB7.2 were simultaneously located on chromosome 7 flanked by 7038 and 7042 at LOD scores 4.34 and 3.76, whileqPWC2.1 andqWCA2.1 were simultaneously located on chromosome 2 flanked by RM492 and RM324 with LOD scores of 2.50 and 3.39. Twelve epistatic combinations were detected for five chalkiness characteristics except for CA. Results indicated that WBA was mainly influenced by the additive effects of main-effect QTLs. PGC and PWC were affected by the effects of epistatic QTLs and the interactions between additive-by-additive effects and the environment. The effects of epistatic QTLs and the main-effect QTLs played important roles on CA, PWB and WCA. For the genetic improvement of grain chalkiness in breeding system, more attention should be paid to epistatic effects and the additive effects of main-effect QTLs.     

QTL detection and MAS selection efficiency for lipid content in brown rice (Oryza sativa L.)

Rice lipid content as one of important ingredients of functional food and industrial products has become an entirely new target in the rice breeding programs worldwide. A genetic linkage map spanning 12 rice chromosomes with an average interval of 10.51 cM between markers was created using 172 DNA markers, which intended to elucidate genetic basis of lipid content in brown rice by QTL detection. Eight QTLs related to lipid content with LOD from 2.52 to 7.86 were mapped on chromosome1, 2, 3, 5, 6, 7 and 9 using a doubled haploid (DH) population from a cross of ‘Samgang/Nagdong’ with field experiments for five years. Two QTLs of qLC5.1 and qLC6.1 in the intervals 5014-5024 and 6011-RM19696 were repeatedly detected over four years at average LOD scores of 4.85 and 4.21, respectively. Five of eight QTLs tend to increase the lipid content from ‘Samgang’ alleles. Epistatic and environmental effects played important roles and explained 42.20% of phenotype variations. Three QTLs of qLC6.1, qLC7.1 and qLC9.1 collectively explained much than 27% of phenotype variations and increased 0.25% of lipid content and, showed much than 85% of selection efficiency for the lines with high lipid contents in the F7 population from a cross of ‘Samgang/Nagdong’. Thus it provides the sufficient possibility to realize QTLs pyramiding and to promote process of rice breeding.     

Identification for quantitative trait loci controlling grain shattering in rice

Seed shattering is an important factor causing loss of grain yield before and during rice harvest. In the present study, the quantitative trait loci regarding shattering scale, breaking tensile strength (BTS) and abscission layer (AL), the parameters evaluating seed shattering habit by hand gripping, a digital force gauge and observation on AL, respectively, were identified by using an doubled haploid line (DHL) population from a cross between a loose-shattering type Tongil variety, ‘Samgang’, and a moderately difficult shattering japonica variety, ‘Nagdong’. Eight QTLs consisted in four QTLs for shattering scale, two QTLs for AL, each one QTL for pulling and bending strength were detected on six chromosomes, respectively. Among them, Qss1 with flanking markers RM6696 and RM476 explained 31% of phenotype variation in shattering scale. Furthermore, two new QTLs controlling shattering habit, Qss5-2 and Qal5-1, were located on chromosome 5 at the interval 5028–5037 and 5021-RM289. They explained 10% and 12% of phenotype variations, respectively. A total of eleven digenic epistatic loci were identified for four parameters. The identification of QTLs affecting seed shattering habits is favorable to thoroughly dissect the genetic mechanism of the shattering habit and to apply for marker-assisted selection in rice breeding system of specific regions.     

Identification of novel recessive gene <Emphasis Type="Italic">xa44</Emphasis>(<Emphasis Type="Italic">t</Emphasis>) conferring resistance to bacterial blight races in rice by QTL linkage analysis using an SNP chip

Key message

Using QTL analysis and fine mapping, the novel recessive gene xa44(t) conferring resistance to BB was identified and the expression level of the gene was confirmed through qRT-PCR analysis.

Abstract

Bacterial blight (BB) disease caused by Xanthomonas oryzae pv. oryzae (Xoo) is a major factor causing rice yield loss in most rice-cultivating countries, especially in Asia. The deployment of cultivars with resistance to BB is the most effective method to control the disease. However, the evolution of new Xoo or pathotypes altered by single-gene-dependent mutations often results in breakdown of resistance. Thus, efforts to identify novel R-genes with sustainable BB resistance are urgently needed. In this study, we identified three quantitative trait loci (QTLs) on chromosomes 1, 4, and 11, from an F₂ population of 493 individuals derived from a cross between IR73571-3B-11-3-K3 and Ilpum using a 7K SNP chip. Of these QTLs, one major QTL, qBB_11, on chromosome 11 explained 61.58% of the total phenotypic variance in the population, with an LOD value of 113.59, based on SNPs 11964077 and 11985463. The single major R-gene, with recessive gene action, was designated xa44(t) and was narrowed down to a 120-kb segment flanked within 28.00 Mbp to 28.12 Mbp. Of nine ORFs present in the target region, two ORFs revealed significantly different expression levels of the candidate genes. These candidate genes (Os11g0690066 and Os11g0690466) are described as “serine/threonine protein kinase domain containing protein” and “hypothetical protein,” respectively. The results will be useful to further understand BB resistance mechanisms and provide new sources of resistance, together with DNA markers for MAS breeding to improve BB resistance in rice.

     

Characterization of allotetraploids derived from protoplast fusion between navel orange and kumquat

In this study, we aimed to produce a citrus fruit with no seed and with edible peel. Therefore, the seedless Yoshida navel oranges (Citrus sinensis ‘Yoshida navel’) and Jangsil kumquat (Fortunella japonica) with edible peel were used as the starting materials. Since two varieties of different genera and different flowering periods would be difficult to crossbreed, protoplast fusion was conducted using the polyethylene glycol method. Yoshida navel orange and Jangsil kumquat were used as an embryogenic callus line and a mesophyll line, respectively. The regenerated plants were analyzed by flow cytometry to identify tetraploids, which were further evaluated by polymerase chain reaction, using simple sequence repeat markers specific for the nuclear and cytoplasmic organellar DNAs of the two parents, to confirm allotetraploids and cybrids. Sixteen allotetraploids were finally produced and characterized phenotypically for leaf morphology and fruit quality. All allotetraploids contained mitochondria originating from Yoshida navel orange; 12 contained chloroplasts derived from navel orange whereas four contained chloroplasts of kumquat origin. We investigated both plant and fruit characteristics of allotetraploids derived from the protoplast fusion of navel orange and kumquat. The sizes of the allotetraploid leaves were intermediate between those of both parents. However, in contrast to the spindle-shaped leaves of both parents, those of the allotetraploids were obovate. Petiole wings were absent in the allotetraploids, a known kumquat trait. Similar to navel oranges, flowering time was mid-May, and pollen was sterile, whereas fruit size, external shape, soluble solids content, and acidity were all intermediate between the two parents. Peel thickness and the number of segments were similar to those of kumquat, and flesh weight was similar to that of navel orange. Collectively, these results indicated that the intergeneric allotetraploids derived from navel orange and kumquat inherited favorable traits of both parents and could be produced and selected despite a lack of extensive parental variation. This is one of the first reports showing fruiting results of protoplast-fused citrus plants. The study reported characteristics of the fruits from both the original plants as well as from the protoplast-fused plant. Detailed characteristics of the allotetraploid fruit produced by protoplast fusion would be very helpful for future polyploid studies.

     

Identification of a rice gene (Bph 1) conferring resistance to brown planthopper (Nilaparvata lugens Stal) using STS markers

This study was carried out to identify a high-resolution marker for a gene conferring resistance to brown planthopper (BPH) biotype 1, using japonica type resistant lines. Bulked segregant analyses were conducted using 520 RAPD primers to identify RAPD fragments linked to the BPH resistance gene. Eleven RAPDs were shown to be polymorphic amplicons between resistant and susceptible progeny. One of these primers, OPE 18, which amplified a 923 bp band tightly linked to resistance, was converted into a sequence-tagged-site (STS) marker. The STS marker, BpE18-3, was easily detectable as a dominant band with tight linkage (3.9cM) to Bph1. It promises to be useful as a marker for assisted selection of resistant progeny in backcross breeding programs to introgress the resistance gene into elite japonica cultivars.     

Development of Molecular Marker to Detect Citrus Melanose Caused by Diaporthe citri from Citrus Melanose-like Symptoms

It is difficult to distinguish melanose and melanoses-like symptoms with the naked eye because they appear similar. To accurately detect melanose symptoms caused by Diaporthe citri from melanose-like symptoms, we developed PCR-based specific primers Dcitri by aligning the internal transcribed spacer (ITS) region of D. citri with the ITS of Diaporthe cytosporella, Diaporthe foeniculina, Colletotrichum gloeosporioides, Botrytis cinerea, Alternaria citri, and Fusarium oxysporum found on citrus peel. PCR results showed that the specific product was amplified in D. citri but not in other isolates including, C. gloeosporioides, B. cinerea, A. citri, F. oxysporum. In addition, specific products were observed in melanose symptoms caused by D. citri but not in melanose-like symptoms, such as copper-injury, sunscald, damages by yellow tea thrips, and pink citrus rust mite. Using the Dcitri primers developed in this study, it is expected that melanose caused by D. citri could be accurately distinguished from melanose-like symptoms.