Marker-Assisted Introgression of Saltol QTL Enhances Seedling Stage Salt Tolerance in the Rice Variety “Pusa Basmati 1”

Marker-assisted selection is an unequivocal translational research tool for crop improvement in the genomics era. Pusa Basmati 1 (PB1) is an elite Indian Basmati rice cultivar sensitive to salinity. Here, we report enhanced seedling stage salt tolerance in improved PB1 genotypes developed through marker-assisted transfer of a major QTL, Saltol. A highly salt tolerant line, FL478, was used as the Saltol donor. Parental polymorphism survey using 456 microsatellite (SSR)/QTL-linked markers revealed 14.3% polymorphism between PB1 and FL478. Foreground selection was carried out using three Saltol-linked polymorphic SSR markers RM8094, RM493, and RM10793 and background selection by 62 genome-wide polymorphic SSR markers. In every backcross generation, foreground selection was restricted to the triple heterozygotes of foreground markers, which was followed by phenotypic and background selections. Twenty-four near isogenic lines (NILs), with recurrent parent genome recovery of 96.0–98.4%, were selected after two backcrosses followed by three selfing generations. NILs exhibited agronomic traits similar to those of PB1 and additional improvement in the seedling stage salt tolerance. They are being tested for per se performance under salt-affected locations for release as commercial varieties. These NILs appear promising for enhancing rice production in salinity-affected pockets of Basmati Geographical Indication (GI) areas of India.

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Foreground selection through SSRs markers for the development of salt tolerant rice variety

Journal of the Bangladesh Agricultural University ◽

10.3329/jbau.v11i1.18215 ◽

2014 ◽

Vol 11 (1) ◽

pp. 67-72 ◽

Cited By ~ 8

Author(s):

U Mondal ◽

MSR Khanom ◽

L Hassan ◽

SN Begum

Keyword(s):

Rice Variety ◽

Rice Cultivar ◽

Susceptible Variety ◽

Recurrent Parent ◽

Salt Tolerant ◽

Foreground Selection ◽

Donor Parent ◽

Ssrs Markers ◽

Level Of Selection ◽

Marker Assisted Backcrossing

Salinity is a great problem for rice production worldwide incurring substantial yield loss; a great threat towards food security. Marker-assisted backcrossing is one of the feasible methods to develop a new salt tolerant rice cultivar to cope with the challenge. The study was focused on to introgress salt tolerant genes from a tolerant rice line, FL-478 to Binadhan-7, an early, agronomically suitable and susceptible variety. Backcrossing was done during boro season; where Binadhan-7 was the recurrent parent and FL-478 was the donor parent. 141 BC1F1 lines were developed, which were subjected to foreground selection; the first level of selection of marker assisted backcrossing program. The aim of foreground selection was to identify the introgressed lines. 141 BC1F1 populations were evaluated with tightly linked salt tolerant markers; AP3206f, RM3412b and RM336. A total of 47 heterozygous BC1F1 lines were selected finally, which have alleles of both of the parents. Those introgressed lines could be efficiently used in further development of a stable early salt tolerant rice variety. DOI: http://dx.doi.org/10.3329/jbau.v11i1.18215 J. Bangladesh Agril. Univ. 11(1): 67-72, 2013

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Application of SSR Technique for the Identification of Markers Linked to Salinity Tolerance in Rice

Progressive Agriculture ◽

10.3329/pa.v19i2.16929 ◽

2013 ◽

Vol 19 (2) ◽

pp. 57-65

Author(s):

MH Kabir ◽

MM Islam ◽

SN Begum ◽

AC Manidas

Keyword(s):

Salt Tolerance ◽

Ssr Markers ◽

Salinity Tolerance ◽

Seedling Stage ◽

Phenotypic Screening ◽

Salt Tolerant ◽

Marker Assisted Breeding ◽

Hydroponic System ◽

Rice Landrace ◽

Salt Susceptible

A cross was made between high yielding salt susceptible BINA variety (Binadhan-5) with salt tolerant rice landrace (Harkuch) to identify salt tolerant rice lines. Thirty six F3 rice lines of Binadhan-5 x Harkuch were tested for salinity tolerance at the seedling stage in hydroponic system using nutrient solution. In F3 population, six lines were found as salt tolerant and 10 lines were moderately tolerant based on phenotypic screening at the seedling stage. Twelve SSR markers were used for parental survey and among them three polymorphic SSR markers viz., OSR34, RM443 and RM169 were selected to evaluate 26 F3 rice lines for salt tolerance. With respect to marker OSR34, 15 lines were identified as salt tolerant, 9 lines were susceptible and 2 lines were heterozygous. While RM443 identified 3 tolerant, 14 susceptible and 9 heterozygous rice lines. Eight tolerant, 11 susceptible and 7 heterozygous lines were identified with the marker RM169. Thus the tested markers could be efficiently used for tagging salt tolerant genes in marker-assisted breeding programme.DOI: http://dx.doi.org/10.3329/pa.v19i2.16929 Progress. Agric. 19(2): 57 - 65, 2008

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Marker aided introgression of ‘Saltol’, a major QTL for seedling stage salinity tolerance into an elite Basmati rice variety ‘Pusa Basmati 1509’

Scientific Reports ◽

10.1038/s41598-020-70664-0 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Ashutosh Kumar Yadav ◽

Aruna Kumar ◽

Nitasha Grover ◽

Ranjith Kumar Ellur ◽

S. Gopala Krishnan ◽

...

Keyword(s):

Salinity Tolerance ◽

Rice Variety ◽

Seedling Stage ◽

Basmati Rice ◽

Major Qtl

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Improved bacterial leaf blight disease resistance in the major elite Vietnamese rice cultivar TBR225 via editing of the OsSWEET14 promoter

PLoS ONE ◽

10.1371/journal.pone.0255470 ◽

2021 ◽

Vol 16 (9) ◽

pp. e0255470

Author(s):

Phuong Nguyen Duy ◽

Dai Tran Lan ◽

Hang Pham Thu ◽

Huong Phung Thi Thu ◽

Ha Nguyen Thanh ◽

...

Keyword(s):

Agronomic Traits ◽

Rice Variety ◽

Rice Cultivar ◽

Leaf Blight ◽

Bacterial Leaf Blight ◽

Transcription Activator ◽

Rice Varieties ◽

Sugar Transporters ◽

Blight Disease ◽

Mutant Lines

TBR225 is one of the most popular commercial rice varieties in Northern Vietnam. However, this variety is highly susceptible to bacterial leaf blight (BLB), a disease caused by Xanthomonas oryzae pv. oryzae (Xoo) which can lead to important yield losses. OsSWEET14 belongs to the SWEET gene family that encodes sugar transporters. Together with other Clade III members, it behaves as a susceptibility (S) gene whose induction by Asian Xoo Transcription-Activator-Like Effectors (TALEs) is absolutely necessary for disease. In this study, we sought to introduce BLB resistance in the TBR225 elite variety. First, two Vietnamese Xoo strains were shown to up-regulate OsSWEET14 upon TBR225 infection. To investigate if this induction is connected with disease susceptibility, nine TBR225 mutant lines with mutations in the AvrXa7, PthXo3 or TalF TALEs DNA target sequences of the OsSWEET14 promoter were obtained using the CRISPR/Cas9 editing system. Genotyping analysis of T0 and T1 individuals showed that mutations were stably inherited. None of the examined agronomic traits of three transgene-free T2 edited lines were significantly different from those of wild-type TBR225. Importantly, one of these T2 lines, harboring the largest homozygous 6-bp deletion, displayed decreased OsSWEET14 expression as well as a significantly reduced susceptibility to a Vietnamese Xoo strains and complete resistance to another one. Our findings indicate that CRISPR/Cas9 editing conferred an improved BLB resistance to a Vietnamese commercial elite rice variety.

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Marker Assisted Development and Characterization of Herbicide Tolerant Near Isogenic Lines of a Mega Basmati Rice Variety, “Pusa Basmati 1121”

Rice ◽

10.1186/s12284-020-00423-2 ◽

2020 ◽

Vol 13 (1) ◽

Author(s):

Nitasha Grover ◽

Aruna Kumar ◽

Ashutosh Kumar Yadav ◽

S. Gopala Krishnan ◽

Ranjith Kumar Ellur ◽

...

Keyword(s):

Genetic Background ◽

Cooking Quality ◽

Rice Variety ◽

Basmati Rice ◽

Recurrent Parent ◽

Quality Traits ◽

Near Isogenic Lines ◽

Isogenic Lines ◽

Herbicide Tolerant ◽

Grain And Cooking Quality

Abstract Background Direct-seeded rice (DSR) is a potential technology for sustainable rice farming as it saves water and labor. However, higher incidence of weed under DSR limits productivity. Therefore, there is a need to develop herbicide tolerant (HT) rice varieties. Results We used marker assisted backcross breeding (MABB) to transfer a mutant allele of Acetohydroxy acid synthase (AHAS) gene, which confers tolerance to imidazolinone group of herbicides from the donor parent (DP) “Robin” into the genetic background of an elite popular Basmati rice variety, Pusa Basmati 1121 (PB 1121). Foreground selection was done using the AHAS gene linked Simple Sequence Repeat (SSR) marker RM6844 and background selection was performed using 112 genome-wide SSR markers polymorphic between PB 1121 and Robin. Phenotypic selection for agronomic, Basmati grain and cooking quality traits in each generation was carried out to improve the recovery of recurrent parent phenome (RPP). Finally, a set of 12 BC4F4 near isogenic lines (NILs), with recurrent parent genome (RPG) recovery ranging from 98.66 to 99.55% were developed and evaluated. PB 1121-HT NILs namely 1979-14-7-33-99-10, 1979-14-7-33-99-15 and 1979-14-7-33-99-66 were found superior to PB 1121 in yield with comparable grain and cooking quality traits and herbicide tolerance similar to Robin. Conclusion Overall, the present study reports successful development of HT NILs in the genetic background of popular Basmati rice variety, PB 1121 by introgression of mutated AHAS allele. This is the first report on the development of HT Basmati rice. Superior NILs are being evaluated in the national Basmati trials, the release of which is likely to provide a viable option for the adoption of DSR technology in Basmati rice cultivation.

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Development of Sakon Nakhon Rice Variety for Blast Resistance through Marker Assisted Backcross Breeding

Agronomy ◽

10.3390/agronomy9020067 ◽

2019 ◽

Vol 9 (2) ◽

pp. 67 ◽

Cited By ~ 3

Author(s):

Nawaporn Srichant ◽

Sompong Chankaew ◽

Tidarat Monkham ◽

Petcharat Thammabenjapone ◽

Jirawat Sanitchon

Keyword(s):

Agronomic Traits ◽

Blast Resistance ◽

Rice Variety ◽

Cropping System ◽

Introgression Line ◽

Phenotypic Selection ◽

Rice Cultivar ◽

Breeding Population ◽

Blast Disease ◽

Resistance Qtls

The Sakon Nakhon (SKN) rice cultivar is non-photosensitive, rich in aroma, and an excellent choice for cooking quality; which adapts well to both upland and lowland conditions. Furthermore, it has been adopted by Thailand’s sugarcane growers, as it has proved fit for an upland crop preceding the sugarcane cropping system. However, SKN is very susceptible to blast disease caused by Pyricularia oryzae. The purpose of this study was to breed SKN for blast resistance, using marker-assisted backcrossing, together with phenotypic selection. The breeding population was constructed by crossing the SKN (recurrent) with the RD6 introgression line (donor), which contained four blast resistant quantitative trait loci (QTLs). Franking microsatellite markers for blast resistance QTLs on chromosomes 1, 2, 11 and 12 were used for selection through BC2F2. Thirteen BC2F3 selected lines were evaluated under greenhouse conditions, and seven lines of BC2F4 were evaluated against blast, along with their agronomic traits, under field conditions (upland and lowland). SKN 39-10-19-29-12 and SKN 39-10-19-29-13 presented high resistance to leaf and neck blast; and were non-photosensitive, with the same agronomic traits as the SKN. This study successfully demonstrates the improvement of the recommended SKN variety blast resistance, while maintaining similar agronomic traits.

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Identification of SSR Markers for Salt-tolerance in Rice Variety CSR10 by Selective Genotyping

Journal of Plant Biochemistry and Biotechnology ◽

10.1007/bf03263301 ◽

2008 ◽

Vol 18 (1) ◽

pp. 87-91 ◽

Cited By ~ 2

Author(s):

Poonam Rana ◽

Sunita Jain ◽

Sheetal Yadav ◽

Navinder Saini ◽

R. K. Jain

Keyword(s):

Salt Tolerance ◽

Ssr Markers ◽

Rice Variety ◽

Selective Genotyping

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Marker assisted development and characterization of herbicide tolerant Near Isogenic Lines of a mega Basmati rice variety, “Pusa Basmati 1121”

10.21203/rs.3.rs-32436/v2 ◽

2020 ◽

Author(s):

Nitasha Grover ◽

Aruna Kumar ◽

Ashutosh Kumar Yadav ◽

Gopala Krishnan S. ◽

Ranjith Kumar Ellur ◽

...

Keyword(s):

Genetic Background ◽

Cooking Quality ◽

Rice Variety ◽

Basmati Rice ◽

Recurrent Parent ◽

Quality Traits ◽

Near Isogenic Lines ◽

Isogenic Lines ◽

Herbicide Tolerant ◽

Grain And Cooking Quality

Abstract Background Direct-seeded rice (DSR) is a potential technology for sustainable rice farming as it saves water and labor. However, higher incidence of weed under DSR limits productivity. Therefore, there is a need to develop herbicide tolerant (HT) rice varieties. Results We used marker assisted backcross breeding (MABB) to transfer a mutant allele of Acetohydroxy acid synthase ( AHAS ) gene, which confers tolerance to imidazolinone group of herbicides from the donor parent (DP) “Robin” into the genetic background of an elite popular Basmati rice variety Pusa Basmati 1121 (PB 1121). Foreground selection was done using the AHAS gene linked Simple Sequence Repeat (SSR) marker RM6844 and background selection was performed using 112 genome-wide SSR markers polymorphic between PB 1121 and Robin. Phenotypic selection for agronomic, Basmati grain and cooking quality traits in each generation was carried out to improve the recovery of recurrent parent phenome (RPP). Finally, a set of 12 BC 4 F 4 near isogenic lines (NILs), with recurrent parent genome (RPG) recovery ranging from 98.66 to 99.55% were developed and evaluated. PB 1121-HT NILs namely 1979-14-7-33-99-10, 1979-14-7-33-99-15 and 1979-14-7-33-99-66 were found superior to PB 1121 in yield with comparable grain and cooking quality traits and herbicide tolerance similar to Robin. Conclusion Overall, the present study reports successful development of HT NILs in the genetic background of popular Basmati rice variety PB 1121 by introgression of mutated AHAS allele. This is the first report on the development of HT Basmati rice. Superior NILs are being evaluated in the national Basmati trials, the release of which is likely to provide a viable option for the adoption of DSR technology in Basmati rice cultivation.

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Development of herbicide-tolerant irrigated rice cultivars

Pesquisa Agropecuária Brasileira ◽

10.1590/s0100-204x2010000700010 ◽

2010 ◽

Vol 45 (7) ◽

pp. 701-708 ◽

Cited By ~ 5

Author(s):

Paulo Hideo Nakano Rangel ◽

Francisco Pereira Moura Neto ◽

Paulo Ricardo Reis Fagundes ◽

Ariano Martins de Magalhães Junior ◽

Orlando Peixoto de Morais ◽

...

Keyword(s):

Agronomic Traits ◽

Rice Cultivar ◽

Recurrent Parent ◽

Germplasm Bank ◽

Irrigated Rice ◽

Distance Analysis ◽

Tolerant Plants ◽

Herbicide Tolerant ◽

Imidazolinone Herbicides ◽

Genetic Distance Analysis

The objective of this work was to develop new irrigated rice lines tolerant to imidazolinone herbicides. The backcross breeding procedure was used to transfer the imidazolinone tolerance allele from mutant 93AS3510 to the recurrent parents 'BRS 7 Taim' and 'BRS Pelota'. Individual herbicide-tolerant plants were selected in each generation, for three backcrossings (RC1 to RC3), followed by three selfing generations (RC3F1 to RC3F3). The best four RC3F3 lines for agronomic traits were genotyped with 44 microsatellite markers. The observed conversion index of the new imidazolinone-tolerant lines varied from 91.86 to 97.67%. Pairwise genetic distance analysis between these lines and 22 accessions from the Embrapa's Rice Germplasm Bank clustered the new lines with their respective recurrent parents, but not with 'IRGA 417', which was originally used as recurrent parent to derive IRGA 422 CL, the only imidazolinone-tolerant irrigated rice cultivar recommended for cultivation in Brazil. Therefore, these lines represent new options of genetically diverse imidazolinone-tolerant rice accessions. Lines CNA10756 ('BRS Sinuelo CL') and CNA10757 will be released for cultivation in the Clearfield irrigated rice production system in Rio Grande do Sul, Brazil.

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Improvement of a RD6 Rice Variety for Blast Resistance and Salt Tolerance through Marker-Assisted Backcrossing

Agronomy ◽

10.3390/agronomy10081118 ◽

2020 ◽

Vol 10 (8) ◽

pp. 1118 ◽

Cited By ~ 1

Author(s):

Korachan Thanasilungura ◽

Sukanya Kranto ◽

Tidarat Monkham ◽

Sompong Chankaew ◽

Jirawat Sanitchon

Keyword(s):

Salt Stress ◽

Salt Tolerance ◽

Agronomic Traits ◽

Blast Resistance ◽

Rice Variety ◽

Gene Pyramiding ◽

Blast Disease ◽

Resistance Qtls ◽

Rice Varieties ◽

Marker Assisted Backcrossing

RD6 is one of the most favorable glutinous rice varieties consumed throughout the north and northeast of Thailand because of its aroma and softness. However, blast disease and salt stress cause decreases in both yield quantity and quality during cultivation. Here, gene pyramiding via marker-assisted backcrossing (MAB) using combined blast resistance QTLs (qBl 1, 2, 11, and 12) and Saltol QTL was employed in solving the problem. To pursue our goal, the RD6 introgression line (RGD07005-12-165-1), containing four blast-resistant QTLs, were crossed with the Pokkali salt tolerant variety. Blast resistance evaluation was thoroughly carried out in the fields, from BC2F2:3 to BC4F4, using the upland short-row and natural field infection methods. Additionally, salt tolerance was validated in both greenhouse and field conditions. We found that the RD6 “BC4F4 132-12-61” resulting from our breeding programme successfully resisted blast disease and tolerated salt stress, while it maintained the desirable agronomic traits of the original RD6 variety. This finding may provide a new improved rice variety to overcome blast disease and salt stress in Northeast Thailand.

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