Breeding of High Cooking and Eating Quality in Rice by Marker-Assisted Backcrossing (MABc) Using KASP Markers.
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ABSTRACT:
SUBMITTER: Kim MS
PROVIDER: S-EPMC8073074 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BACKGROUND:Rice blast caused by Magnaporthe oryzae is one of the most widespread biotic constraints that threaten rice production. Using major resistance genes for rice blast resistance improvement is considered to be an efficient and technically feasible approach to achieve optimal grain yield. RESULTS:We report here the introgression of the broad-spectrum blast resistance gene Pi2 into the genetic background of an elite PTGMS line, Feng39S, for enhancing it and its derived hybrid blast resistance through marker-assisted backcrossing (MABC) coupled with genomics-based background selection. Two PTGMS lines, designated as DB16206-34 and DB16206-38, stacking homozygous Pi2 were selected, and their genetic background had recurrent parent genome recovery of 99.67% detected by the SNP array RICE6K. DB16206-34 and DB16206-38 had high resistance frequency, with an average of 94.7%, when infected with 57 blast isolates over 2 years, and the resistance frequency of their derived hybrids ranged from 68.2% to 95.5% under inoculation of 22 blast isolates. The evaluation of results under natural blast epidemic field conditions showed that the selected PTGMS lines and their derived hybrids were resistant against leaf and neck blast. The characterizations of the critical temperature point of fertility-sterility alternation of the selected PTGMS lines, yield, main agronomic traits, and rice quality of the selected PTGMS lines and their hybrids were identical to those of the recurrent parent and its hybrids. DB16206-34/9311 or DB16206-38/9311 can be used as a blast-resistant version to replace the popular hybrid Fengliangyou 4. Likewise, DB16206-34/FXH No.1 or DB16206-38/FXH No.1 can also be used as a blast-resistant version to replace another popular hybrid Fengliangyou Xiang 1. CONCLUSIONS:Our evaluation is the first successful case to apply MABC with genomics-based background selection to improve the blast resistance of PTGMS lines for two-line hybrid rice breeding.
| S-EPMC6733936 | biostudies-literature
Project description:The development of new improved varieties is one of the major goals of plant breeding. Concomitantly, the demand for stable, eco-friendly, and high-quality rice production is constantly increasing. However, most farmers prefer to cultivate familiar rice varieties developed more than 10 years ago to minimize economic risk. A strategy is needed to develop rice varieties without the limitations of the preferred old varieties. Here, we tested the rapid development of near isogenic lines (NILs) using a rapid generation advance system together with marker-assisted backcrossing to overcome the shortcomings of parental materials. For this purpose, we chose rice stripe virus (RSV) susceptible variety Unkwang and RSV resistant variety Haedamssal as experimental materials. First, we backcrossed and screened BC1F1 and BC2F1 plants having similar agronomic traits as Unkwang and the heterozygous genotype for RSV resistant specific marker InDel7 from Haedamssal. Secondly, the genetic background of 11 BC2F1 plants was identified with 73 KASP markers; plants of line YR32548-8 showed 84.5% of recovery of the recurrent parent genome. Among 28 BC2F2 plants, YR32548-8-16 was the line that showed maximum recovery of the recurrent parent genome (96.2%) while effectively introgressed with RSV-resistance loci on chromosome 11. Finally, we selected line YR32548-8-16 as an NIL showing an RSV resistant phenotype and similar agronomic traits to Unkwang. This fast breeding approach will be useful in rice breeding programs for the improvement of varieties preferred by farmers for their stress tolerance, yield, or quality.
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Project description:Rice breeding programs in Hokkaido over the past 100 years have dramatically increased productivity and improved the eating quality of rice. Commercial varieties with high yield and good eating quality, such as Kirara 397, Hoshinoyume, and Nanatsuboshi, have been continuously registered since 1990. Furthermore, varieties with better eating quality using Wx1-1, which reduces amylose content to improve the taste of sticky rice, such as Oborozuki and Yumepirika, were registered in 2006 and 2008, respectively. However, to the best of our knowledge the genomic changes associated with these improvements have not been determined. Better understanding of the relationships between DNA sequences and agricultural traits could facilitate rice breeding programs in Hokkaido. Marker-assisted selection (MAS), which can select the plants with chromosomal regions tagged with DNA markers for desirable traits, is an advanced technology to manage genetic improvements. Here, we summarize the current states of MAS in rice breeding programs in Hokkaido before huge data sets of genome sequences using next-generation sequencing technology come into practical use in rice breeding programs.
| S-EPMC6776137 | biostudies-literature
Project description:The eating quality of cooked rice is important and determines its market price and consumer acceptance. To comprehensively describe the variation of eating quality in 183 rice germplasm accessions, we evaluated 33 eating-quality traits including amylose and protein contents, pasting properties of rice flour, and texture of cooked rice grains. All eating-quality traits varied widely in the germplasm accessions. Principal-components analysis (PCA) revealed that allelic differences in the Wx gene explained the largest proportion of phenotypic variation of the eating-quality traits. In 146 accessions of non-glutinous temperate japonica rice, PCA revealed that protein content and surface texture of the cooked rice grains significantly explained phenotypic variations of the eating-quality traits. An allelic difference based on simple sequence repeats, which was located near a quantitative trait locus (QTL) on the short arm of chromosome 3, was associated with differences in the eating quality of non-glutinous temperate japonica rice. These results suggest that eating quality is controlled by genetic factors, including the Wx gene and the QTL on chromosome 3, in Japanese rice accessions. These genetic factors have been consciously selected for eating quality during rice breeding programs in Japan.
| S-EPMC4785008 | biostudies-literature
Project description:Few public sector rice breeders have the capacity to use NGS-derived markers in their breeding programmes despite rapidly expanding repositories of rice genome sequence data. They rely on > 18,000 mapped microsatellites (SSRs) for marker-assisted selection (MAS) using gel analysis. Lack of knowledge about target SNP and InDel variant loci has hampered the uptake by many breeders of Kompetitive allele-specific PCR (KASP), a proprietary technology of LGC genomics that can distinguish alleles at variant loci. KASP is a cost-effective single-step genotyping technology, cheaper than SSRs and more flexible than genotyping by sequencing (GBS) or array-based genotyping when used in selection programmes. Before this study, there were 2015 rice KASP marker loci in the public domain, mainly identified by array-based screening, leaving large proportions of the rice genome with no KASP coverage. Here we have addressed the urgent need for a wide choice of appropriate rice KASP assays and demonstrated that NGS can detect many more KASP to give full genome coverage. Through re-sequencing of nine indica rice breeding lines or released varieties, this study has identified 2.5 million variant sites. Stringent filtering of variants generated 1.3 million potential KASP assay designs, including 92,500 potential functional markers. This strategy delivers a 650-fold increase in potential selectable KASP markers at a density of 3.1 per 1 kb in the indica crosses analysed and 377,178 polymorphic KASP design sites on average per cross. This knowledge is available to breeders and has been utilised to improve the efficiency of public sector breeding in Nepal, enabling identification of polymorphic KASP at any region or quantitative trait loci in relevant crosses. Validation of 39 new KASP was carried out by genotyping progeny from a range of crosses to show that they detected segregating alleles. The new KASP have replaced SSRs to aid trait selection during marker-assisted backcrossing in these crosses, where target traits include rice blast and BLB resistance loci. Furthermore, we provide the software for plant breeders to generate KASP designs from their own datasets.
| S-EPMC5842261 | biostudies-literature
Project description:The effect of nitrogen fertilizer application on the quality of rice post-storage is not well understood. The eating and cooking quality (ECQ) of rice treated with 0 (CK, control), 160 (IN, insufficient nitrogen), 260 (AN, adequate nitrogen), and 420 (EN, excessive nitrogen) kg N/ha was analyzed over 12 months of storage. Results showed that the rate of nitrogen fertilizer application had no significant impact on the changes in taste value during storage. However, EN application significantly increased the hardness (p < 0.05), reduced the gumminess (p < 0.05), and delayed the decline in the viscosity of rice paste by two months after one-year storage, compared with other treatments. In conclusion, although EN application resulted in an inferior texture of rice, it delayed the quality change by two months during storage. It was demonstrated that a rational nitrogen application rate (0-260 kg N/ha) for rice cultivation is particularly important to obtain high ECQ; however, EN may be beneficial for the stability of the ECQ during storage.
| S-EPMC8213157 | biostudies-literature
Project description:Phospholipids belong to a significant class of lipids and comprise ~10% of total lipids in rice grains. Lysophospholipid (LPL) is derived from the hydrolysis of phospholipids and plays an important role in rice grain quality. Our previous study demonstrated that mutations in a phospholipase D gene (OsPLD?1) significantly altered lipid metabolites and reduced phytic acid content. In the present study, the effect of two ospld?1 mutations on LPL and other physicochemical prosperities of brown rice was further investigated, with the aim of assessing the overall importance of ospld?1 mutations in rice grain quality. Metabolite profiling revealed a ~15% increase in LPL level in both ospld?1 mutants as compared with their wild-type (WT) parent. Both ospld?1 mutations significantly lowered the apparent amylose content in brown rice flour (~1.9%) and altered viscosity profiles with significantly increased breakdown (+12.4%) and significantly reduced setback viscosity (-6.2%). Moreover, both ospld?1 mutations significantly lowered the gelatinization onset, peak temperature and retrogradation percentage of brown rice flour. This study demonstrated that OsPLD?1 plays a crucial role in rice grain quality and its mutation could, in general, improve the cooking and eating quality and nourishment of brown rice.
| S-EPMC7154823 | biostudies-literature
Project description:In rice (Oryza sativa), amylose content (AC) is the major factor that determines eating and cooking quality (ECQ). The diversity in AC is largely attributed to natural allelic variation at the Waxy (Wx) locus. Here we identified a rare Wx allele, Wxmw , which combines a favorable AC, improved ECQ and grain transparency. Based on a phylogenetic analysis of Wx genomic sequences from 370 rice accessions, we speculated that Wxmw may have derived from recombination between two important natural Wx alleles, Wxin and Wxb . We validated the effects of Wxmw on rice grain quality using both transgenic lines and near-isogenic lines (NILs). When introgressed into the japonica Nipponbare (NIP) background, Wxmw resulted in a moderate AC that was intermediate between that of NILs carrying the Wxb allele and NILs with the Wxmp allele. Notably, mature grains of NILs fixed for Wxmw had an improved transparent endosperm relative to soft rice. Further, we introduced Wxmw into a high-yielding japonica cultivar via molecular marker-assisted selection: the introgressed lines exhibited clear improvements in ECQ and endosperm transparency. Our results suggest that Wxmw is a promising allele to improve grain quality, especially ECQ and grain transparency of high-yielding japonica cultivars, in rice breeding programs.
| S-EPMC8246539 | biostudies-literature
Project description: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, qDTY3.1 , qDTY6.1 , and qDTY6.2 , 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 qDTY3.1 to be the largest and most consistent QTL affecting yield under drought conditions, followed by qDTY6.1 and qDTY6.2 , respectively. QTL class analysis also showed that lines with a combination of qDTY3.1 and qDTY6.1 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.
| S-EPMC5670188 | biostudies-other
Project description:Cooked rice of 'Sasanishiki' is soft and not as sticky as those of Japanese leading cultivars 'Koshihikari' and 'Hitomebore'. As a method for efficient selection of a breeding line having a good eating quality like that of 'Sasanishiki', the use of physical properties of cooked rice and cooking quality was examined. There were differences of physical properties of the surface layer, starch-iodine blue value per solid substance weight in cooking water and volume expansion of cooked rice between 'Sasanishiki' and 'Hitomebore', these properties being considered to be usable for the selection of breeding lines. Using these traits as selection targets, one line, named 'Tohoku 194', which has eating quality highly similar to that of 'Sasanishiki' and cold tolerance derived from 'Hitomebore', was selected from progeny of a cross between 'Sasanishiki' and 'Hitomebore'. An application for registration as a new variety has been submitted for 'Tohoku 194' under the Japanese Plant Variety Protection Act, and is expected to become a recommended cultivar in Miyagi Prefecture. 'Tohoku 194' may fulfill various demands of consumers and companies in the food industry.
| S-EPMC3688386 | biostudies-literature