QTL mapping of a tolerance gene for germination under anaerobic conditions in rice

Suk-Man Kim,Endang Septiningsih,Kyung-Ho Kang,Bo-Kyeong Kim,Nguyen Thi Lang,Russell Reinke 한국육종학회 2014 한국육종학회 심포지엄 Vol.2014 No.07

Rice cultivation by direct seeding allows reduced labour and production costs in addition to other benefits. However the success of this rice production method can be limited by uneven fields with poor drainage or heavy rainfall at sowing leading to early flooding conditions slowing germination and hindering crop establishment. Hence, the need to improve tolerance to anaerobic conditions in both rainfed and irrigated rice ecosystem after direct seeding. In this study QTL analysis was performed to identify QTLs associated with tolerance derived from Vietnamese variety Tai Nguyen (TN) under anaerobic conditions during germination. The population derived from a cross between TN (tolerance indica lines) and Anda (susceptible japonica), was used for collection of phenotypic data based on the survival rates of the seedlings at 21 days after sowing under 10cm of water. A total of 286 F2:3 families of the population were used for QTL mapping and the genotyping was carried out with the infinium 6K SNP-chip based on the illumina infinium platform. Two significant QTLs associated with the AG trait were detected on chromosomes 1 and 11, respectively. In Particular, the QTL on chromsome 1 had an LOD score of 7.45 and R2 of 14.21%. We plan to confirm the identified QTLs in further studies and develop varieties with improved anaerobic germination ability using advanced backcross lines.

Mapping of Quantitative Trait Loci for Yield and Grade Related Traits in Peanut (Arachis hypogaea L.) Using High-Resolution SNP Markers

Yuya Liang,Michael R. Baring,Endang M. Septiningsih 한국육종학회 2018 Plant Breeding and Biotechnology Vol.6 No.4

Yield and grade are the key factors that affect production value of peanut. The objective of this study was to identify QTLs for pod yield, hundred-seed weight, and total sound mature kernel (TSMK). A total of 90 recombinant inbred lines, derived from Tamrun OL07 and a breeding line Tx964117, were used as a mapping population and planted in Brownfield and Stephenville, Texas. A genetic map was developed using 1,211 SNP markers based on double digest restriction-site associated DNA sequencing (ddRAD-seq). A total of 10 QTLs were identified above the permutation threshold, three for yield, three for hundred-seed weight and four for TSMK, with LOD score values of 3.7 - 6.9 and phenotypic variance explained of 12.2% - 35.9%. Among those, there were several QTLs that were detected in more than one field experiment. The commonly detected QTLs in this study may be used as potential targets for future breeding program to incorporate yield and grade related traits through molecular breeding.

Evaluation of SSR and SNP Markers for Molecular Breeding in Rice

( Zennia Jean Gonzaga ),( Kashif Aslam ),( Endang M. Septiningsih ),( Bertrand C. Y. Collard ) 한국육종학회 2015 Plant Breeding and Biotechnology Vol.3 No.2

Simple sequence repeats (SSRs) have been the marker of choice for rice molecular breeding due to the high level of polymorphism, technical simplicity and low cost. Recent advances in rice genomics have led to the discovery of abundant single nucleotide polymorphism (SNPs) which have enormous potential for rice molecular breeding. To assess both marker systems for molecular breeding in rice, SSR and SNP markers were evaluated on a set of 23 genotypes representing indica germplasm for their usefulness in molecular research and breeding program. Seven hundred SSR and sequence tagged sites (STS) markers and 384 SNPs were screened for polymorphism. Highly polymorphic markers based on polymorphic information content (PIC) values were identified, which will be useful for molecular breeding. Data was used to identify an “indica genotyping set” based on high level of polymorphism, chromosome position and marker quality which will provide kits of markers for marker assisted selection (MAS). Genetic diversity analysis using SSR data was more consistent with pedigrees compared to analysis with SNP data indicating that more than 384 SNPs are required when elite indica breeding material is used. The results also indicated that there were polymorphic “blind spots” for the fixed SNP set suggesting that SSRs could still be used to complement fixed-SNP genotyping platforms for some molecular breeding applications.

Mapping QTLs for Leafspot Resistance in Peanut Using SNP-Based Next-Generation Sequencing Markers

( Yuya Liang ),( Michael Baring ),( Shichen Wang ),( Endang M. Septiningsih ) 한국육종학회 2017 Plant Breeding and Biotechnology Vol.5 No.2

Leafspot is one of the major diseases of peanut (Arachis hypogaea L.) that can cause more than 50% yield loss. The objective of this study was to identify and map quantitative trait loci (QTLs) for resistance to leafspot disease. An F2:6 recombinant inbred line (RIL) population, derived from a released cultivar Tamrun OL07 and a highly tolerant breeding line Tx964117, were used as a mapping population. A total of 90 RILs were planted for disease phenotyping in Yoakum, Texas in 2010 and 2012. A genetic map spanning the 20 linkage groups was developed using 1,211 SNP markers based on double digest restriction-site associated DNA sequencing (ddRAD-seq). A total of six quantitative trait loci (QTLs) were identified, with LOD score values of 3.2-5.0 and phenotypic variance explained ranging from 11%-24%. Major QTLs identified in this study may be used as potential targets for peanut improvement to leafspot disease through molecular breeding.

Development of Improved Ciherang-Sub1 Having Tolerance to Anaerobic Germination Conditions

( Anna Mariel U. Toledo ),( John Carlos I. Ignacio ),( Carlos Casal Jr ),( Zennia Jean Gonzaga ),( Merlyn S. Mendioro ),( Endang M. Septiningsih ) 한국육종학회 2015 Plant Breeding and Biotechnology Vol.3 No.2

The increased severity and frequency of flooding is causing greater yield reductions in most rice-growing areas. To address this, popular cultivars were improved through introgression of SUB1, an FR13A-derived QTL conferring submergence tolerance at the vegetative stage, using marker-assisted backcrossing (MABC). Ciherang-Sub1, one of these improved near isogenic lines (NILs), showed significantly higher tolerance compared to the original cultivar while retaining its desirable agronomic qualities. However, due to the current shift to direct seeding, seed germination may also be adversely affected by flooding; thus the addition of major QTLs which can confer anaerobic germination (AG) tolerance will be highly beneficial. The AG tolerance QTL, qAG-9-2, also referred to as AG1, derived from Khao Hlan On, a Myanmar landrace, has been introgressed into the elite cultivar IR64 to produce IR64-AG1. This research focused on the transfer of AG1 to Ciherang-Sub1 via MABC, using IR64-AG1, a closely-related donor. Introgression of AG1 and recovery of the Ciherang genome was done in two backcross generations followed by one generation of selfing. The use of a closely-related donor shortened the development period to two years which could have been further reduced if a larger BC1F1 population had been used. Phenotypic evaluation showed that introgression of AG1 significantly increased AG tolerance compared to Ciherang-Sub1, and that the newly developed Ciherang-Sub1+AG1 retained the submergence tolerance from SUB1. The approach is very promising for faster development of improved lines using closely-related cultivars or improved lines as donors for introducing key traits.

Development of High-Yielding Rice Varieties Suitable for Swampy Lands in Indonesia

( Indrastuti A. Rumanti ),( Yudhistira Nugraha ),( Rina H. Wening ),( Zennia Jean C. Gonzaga ),( Suwarno ),( Anggiani Nasution ),( Dede Kusdiaman ),( Endang M. Septiningsih ) 한국육종학회 2016 Plant Breeding and Biotechnology Vol.4 No.4

Productivity of swampy land rice varieties in Indonesia remains low due to abiotic and biotic stresses. Iron toxicity, submergence and long-term flooding are common problems that affect plant growth, sometimes leading to total crop loss. Meanwhile, rice blast, rice tungro virus (RTV), and bacterial leaf blight (BLB) can also lead to severe yield loss. These stresses could be overcome by an integrative approach of cultural practices and planting multi-stress tolerant rice. Here we describe the development of new high-yielding varieties that are adapted to the swampy land environments in Indonesia with multi-stress tolerance to diverse abiotic and biotic stresses. Multi-environmental trials were performed in nine locations to screen for several abiotic and biotic stresses in the field and greenhouse in 2012 and 2013. This study identified promising rice lines that had high grain yield as well as tolerance to iron toxicity and submergence, resistance to BLB and RTV, and good grain quality. The best line was B11377F-MR-34-2, derived from a double cross among Cinglonik, IRBB7, Mamberamo and IR64. It was confirmed that this advanced breeding line carries the submergence tolerance gene, SUB1, through expression analysis of the SUB1A gene. Another promising line was B11586F-MR-11-2-2, having iron toxicity tolerance, resistance to RTV, and high milling recovery. Moreover, these lines have passed the Indonesian national variety release committee and have been named as Inpara8 and Inpara9, and are targeted for dissemination and adoption in the swampy areas.