Multiplex PCR genotyping for five bacterial blight resistance genes applied to marker‐assisted selection in rice (<i>Oryza sativa</i>)

Yap, Ruishen; Hsu, Yu-Chia; Wu, Yong-Pei; Lin, Yi Ru; Kuo, Chei-Wei

doi:10.1111/pbr.12368

Cited by 25 publications

(26 citation statements)

References 35 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…To date, 42 BB resistance genes have been identified from diverse sources, of which Xa4, xa5, Xa7, xa13 and Xa21 are most frequently utilized in BB resistance breeding programs [5][6][7]. Although the BB resistance genes xa5 and xa13 are recessive in nature, abundant molecular marker resources allow for molecular marker-assisted breeding [8][9][10][11]. The xa5 gene encodes a mutated gamma subunit of basal transcription factor IIA 5 (TFIIAγ5), and along with the dominant resistance gene Xa7, has shown strong resistance to a virulent BB strain, Z-173, in China [11,12].…”

Section: Introductionmentioning

confidence: 99%

Pyramiding Bacterial Blight Resistance Genes in Tainung82 for Broad-Spectrum Resistance Using Marker-Assisted Selection

Hsu

Chiu²,

Yap

et al. 2020

IJMS

Self Cite

View full text Add to dashboard Cite

Tainung82 (TNG82) is one of the most popular japonica varieties in Taiwan due to its relatively high yield and grain quality, however, TNG82 is susceptible to bacterial blight (BB) disease. The most economical and eco-friendly way to control BB disease in japonica is through the utilization of varieties that are resistant to the disease. In order to improve TNG82’s resistance to BB disease, five bacterial blight resistance genes (Xa4, xa5, Xa7, xa13 and Xa21) were derived from a donor parent, IRBB66 and transferred into TNG82 via marker-assisted backcrossing breeding. Five BB-resistant gene-linked markers were integrated into the backcross breeding program in order to identify individuals possessing the five identified BB-resistant genes (Xa4, xa5, Xa7, xa13 and Xa21). The polymorphic markers between the donor and recurrent parent were used for background selection. Plants having maximum contribution from the recurrent parent genome were selected in each generation and crossed with the recipient parent. Selected BC3F1 plants were selfed in order to generate homozygous BC3F2 plants. Nine pyramided plants, possessing all five BB-resistant genes, were obtained. These individuals displayed a high level of resistance against the BB strain, XF89-b. Different BB gene pyramiding lines were also inoculated against the BB pathogen, resulting in more than three gene pyramided lines that exhibited high levels of resistance. The five identified BB gene pyramided lines exhibited yield levels and other desirable agronomic traits, including grain quality and palatability, consistent with TNG82. Bacterial blight-resistant lines possessing the five identified BB genes exhibited not only higher levels of resistance to the disease, but also greater yield levels and grain quality. Pyramiding multiple genes with potential characteristics into a single genotype through marker-assisted selection can improve the efficiency of generating new crop varieties exhibiting disease resistance, as well as other desirable traits.

show abstract

Section: Introductionmentioning

confidence: 99%

Pyramiding Bacterial Blight Resistance Genes in Tainung82 for Broad-Spectrum Resistance Using Marker-Assisted Selection

Hsu

Chiu²,

Yap

et al. 2020

IJMS

Self Cite

View full text Add to dashboard Cite

show abstract

“…Recently, numerous advanced breeding lines introduced from IRRI and wild relatives have been used in breeding programs to improve biotic and abiotic stresses for sustainable agriculture, e. g. IRBB66 pyramided with 5 bacterial blight resistant genes (Yap et al 2016). Thus, current rice breeding goals in Taiwan emphasize grain quality rst, followed by other traits such as resistances and multi-dimensional utilizations (forage and landscape).…”

Section: Unveiling Taiwanese Rice Germplasmmentioning

confidence: 99%

Genetic Diversity of Landraces and Improved Varieties of Rice (Oryza sativa L.) in Taiwan

Hour

Hsieh

Chang

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

Background: Rice, the most important crop in Asia, has been cultivated in Taiwan for more than 5,000 years. The landraces preserved by indigenous peoples and brought by immigrants from China hundreds of years ago exhibit large variation in morphology, implying that they comprise rich genetic resources. Breeding goals according to the preferences of farmers, consumers and government policies also alter gene pools and genetic diversity of improved varieties. To unveil how genetic diversity is affected by natural, farmers’, and breeders’ selections is crucial for germplasm conservation and crop improvement.Results: A diversity panel of 148 rice accessions, including 47 cultivars and 59 landraces from Taiwan and 42 accessions from other countries, were genotyped by using 75 molecular markers that revealed an average of 12.7 alleles per locus with mean polymorphism information content of 0.72. These accessions could be grouped into five subpopulations corresponding to wild rice, japonica landraces, indica landraces, indica cultivars and japonica cultivars. The genetic diversity within subpopulations was: wild rices > landraces > cultivars; and indica rice > japonica rice. Despite having less variation among cultivars, japonica landraces had greater genetic variation than indica landraces because the majority of Taiwanese japonica landraces preserved by indigenous peoples were classified as tropical japonica. Two major clusters of indica landraces were formed by phylogenetic analysis, in accordance with immigration from two origins. Genetic erosion had occurred in later japonica varieties due to a narrow selection of germplasm being incorporated into breeding programs for premium grain quality. Genetic differentiation between early and late cultivars was significant in japonica (FST = 0.3751) but not in indica (FST = 0.0045), indicating effects of different breeding goals on modern germplasm. Indigenous landraces with unique intermediate and admixed genetic backgrounds were untapped, representing valuable resources for rice breeding.Conclusions: The genetic diversity of improved rice varieties has been substantially shaped by breeding goals, leading to differentiation between indica and japonica cultivars. Taiwanese landraces with different origins possess various and unique genetic backgrounds. Taiwanese rice germplasm provides diverse genetic variation for association mapping to unveil useful genes and is a precious genetic reservoir for rice improvement.

show abstract

“…Multiplexed PCR was carried out to assay alleles of the BLB resistance genes Xa21 and Xa4 in a single tube PCR using the new primer pair ABUOP0001_F/R, and the marker Xa4_F/R [31], respectively. Of the IRBB lines, IRBB 21 (known-to-carry the resistance allele at Xa21; known-to-carry the susceptible allele at Xa4), IRBB 62 (known-to-carry the resistance allele at both Xa21 and Xa4) and IRBB 4…”

Section: High Throughput Screening Assaysmentioning

confidence: 99%

A novel intragenic marker targeting the ectodomain of bacterial leaf blight resistance gene Xa21 in rice

Nanayakkara¹,

Edirisingha²,

Dissanayake³

et al. 2019

Preprint

View full text Add to dashboard Cite

Background Among the diseases in rice (Oryza sativa L.), bacterial leaf blight (BLB) caused by Xanthomonas oryzae pv. oryzae results in devastating economic losses, both in terms of yield and quality. The Xa21 mapped to the rice chromosome 11, is known to convey resistance against BLB by its involvement in plant pathogen recognition and immunity responses. The closely-linked sequence-tagged site marker pTA248 is frequently used for marker-assisted selection (MAS) of Xa21. However, lower precision and linkage drag of linked-markers hinders the reliability and effectiveness in MAS compared to the use of flanking or intergenic markers. Results In the current study, a diagnostic intragenic marker was developed for MAS of Xa21 in rice. The new marker ABUOP0001 targets a 19-bp insertion/deletion (InDel) on the ectodomain of the Xa21, and amplifies a 200-bp amplicon from the rice line IRBB 62, which is known-to-carry the ‘resistance allele’, and a 181-bp amplicon from IRBB 7, which is known-to-carry the ‘susceptible allele’. The resistance allele was identified in ten IRBB lines, and five newly improved Sri Lankan rice accessions through ABUOP0001 marker assay. In a field study, 14 of these accessions conveyed highly resistant BLB disease responses, and one conveyed an intermediate response. While carrying the susceptible allele at Xa21, 30 accessions conveyed a resistance response to BLB, and it could be due to the contribution of other Xa resistance alleles in their genetic background. Further, the Xa21 resistance allele was identified in 1,675 rice accessions through an in silico analysis of genomic sequences available through the 3K Rice Genomes Project. The intragenic marker ABUOP0001 performs equally to that of the linked-marker pTA248 anchored 224 kbp upstream of Xa21, in detecting resistant and susceptible BLB phenotypes. The marker ABUOP0001 is compatible for high-throughput screening with high resolution melting (HRM) and can be multiplexed effectively with an intragenic marker of BLB resistance gene Xa4. Conclusion The marker ABUOP0001 is a diagnostic intragenic marker that can be recommended for MAS of Xa21 in rice. The marker can be assayed as a high-throughput marker using HRM and multiplexed PCR.

show abstract

Multiplex PCR genotyping for five bacterial blight resistance genes applied to marker‐assisted selection in rice (Oryza sativa)

Cited by 25 publications

References 35 publications

Pyramiding Bacterial Blight Resistance Genes in Tainung82 for Broad-Spectrum Resistance Using Marker-Assisted Selection

Pyramiding Bacterial Blight Resistance Genes in Tainung82 for Broad-Spectrum Resistance Using Marker-Assisted Selection

Genetic Diversity of Landraces and Improved Varieties of Rice (Oryza sativa L.) in Taiwan

A novel intragenic marker targeting the ectodomain of bacterial leaf blight resistance gene Xa21 in rice

Contact Info

Product

Resources

About