Linkage map construction and quantitative trait loci (QTL) mapping using intermated vs. selfed recombinant inbred maize line (Zea mays L.)

Khanal, R., Navabi, A. and Lukens, L. 2015. Linkage map construction and quantitative trait loci (QTL) mapping using intermated vs. selfed recombinant inbred maize line (Zea mays L.). Can. J. Plant Sci. 95: 1133–1144. Intermating of individuals in an F2 population increases genetic recombination between markers, which is useful for linkage map construction and quantitative trait loci (QTL) mapping. The objectives of this study were to compare the linkage maps and precision of QTL detection in an intermated recombinant inbred line (IRIL) population and a selfed recombinant inbred line (RIL) population. Both, IRIL and RIL, populations were developed from Zea mays inbred lines CG60 and CG102. The populations were grown in two environments to evaluate traits, and inbred lines from each population were genotyped with SSR and SNP markers for linkage map construction and QTL identification. In addition, we simulated RIL and IRIL populations from two inbred parents to compare the precision of QTL detection between simulated RIL and IRIL populations. In the empirical study, the linkage map was longer in RIL as compared with IRIL, and the average QTL support interval was reduced by 1.37-fold in the IRIL population compared with the RIL population. We detected 16 QTL for flowering time, plant height, leaf number, and stay green in at least one recombinant inbred line population. Two out of 16 QTL were shared between two recombinant inbred line populations. In the simulation study, the QTL support interval was reduced by 1.66-fold in the IRIL population as compared with the RIL population and linked QTL were identified more frequently in IRIL population as compared with RIL population. This study supports the utility of intermated RIL populations for precise QTL mapping.

Download Full-text

Analyzing Quantitative Trait Loci for Fiber Quality and Yield-Related Traits From a Recombinant Inbred Line Population With Gossypium hirsutum Race palmeri as One Parent

Frontiers in Plant Science ◽

10.3389/fpls.2021.817748 ◽

2022 ◽

Vol 12 ◽

Author(s):

Xueying Liu ◽

Le Yang ◽

Jinxia Wang ◽

Yaqing Wang ◽

Zhongni Guo ◽

...

Keyword(s):

Quantitative Trait Loci ◽

Gossypium Hirsutum ◽

Inbred Line ◽

Recombinant Inbred Line ◽

Quantitative Trait ◽

Recombinant Inbred ◽

Fiber Quality ◽

Cotton Breeding ◽

Ril Population ◽

Trait Loci

Fiber quality and yield-related traits are important agronomic traits in cotton breeding. To detect the genetic basis of fiber quality and yield related traits, a recombinant inbred line (RIL) population consisting of 182 lines was established from a cross between Gossypium hirsutum cultivar CCRI35 and G. hirsutum race palmeri accession TX-832. The RIL population was deeply genotyped using SLAF-seq and was phenotyped in six environments. A high-density genetic linkage map with 15,765 SNP markers and 153 SSR markers was constructed, with an average distance of 0.30 cM between adjacent markers. A total of 210 fiber quality quantitative trait loci (QTLs) and 73 yield-related QTLs were identified. Of the detected QTLs, 62 fiber quality QTLs and 10 yield-related QTLs were stable across multiple environments. Twelve and twenty QTL clusters were detected on the At and Dt subgenome, respectively. Twenty-three major QTL clusters were further validated through associated analysis and five candidate genes of four stable fiber quality QTLs were identified. This study revealed elite loci influencing fiber quality and yield and significant phenotypic selection regions during G. hirsutum domestication, and set a stage for future utilization of molecular marker assisted breeding in cotton breeding programs.

Download Full-text

Multi-Environment Quantitative Trait Loci Mapping for Grain Iron and Zinc Content Using Bi-parental Recombinant Inbred Line Mapping Population in Pearl Millet

Frontiers in Plant Science ◽

10.3389/fpls.2021.659789 ◽

2021 ◽

Vol 12 ◽

Author(s):

Tripti Singhal ◽

C. Tara Satyavathi ◽

S. P. Singh ◽

Aruna Kumar ◽

S. Mukesh Sankar ◽

...

Keyword(s):

Quantitative Trait Loci ◽

Linkage Map ◽

Candidate Genes ◽

Pearl Millet ◽

Inbred Line ◽

Recombinant Inbred Line ◽

Quantitative Trait ◽

Recombinant Inbred ◽

Zn Content ◽

Ril Population

Pearl millet is a climate-resilient, nutritious crop with low input requirements that could provide economic returns in marginal agro-ecologies. In this study, we report quantitative trait loci (QTLs) for iron (Fe) and zinc (Zn) content from three distinct production environments. We generated a genetic linkage map using 210 F6 recombinant inbred line (RIL) population derived from the (PPMI 683 × PPMI 627) cross using genome-wide simple sequence repeats (SSRs). The molecular linkage map (seven linkage groups) of 151 loci was 3,273.1 cM length (Kosambi). The content of grain Fe in the RIL population ranged between 36 and 114 mg/Kg, and that of Zn from 20 to 106 mg/Kg across the 3 years (2014–2016) at over the three locations (Delhi, Dharwad, and Jodhpur). QTL analysis revealed a total of 22 QTLs for grain Fe and Zn, of which 14 were for Fe and eight were for Zn on three consecutive years at all locations. The observed phenotypic variance (R2) explained by different QTLs for grain Fe and Zn content ranged from 2.85 (QGFe.E3.2014–2016_Q3) to 19.66% (QGFe.E1.2014–2016_Q3) and from 2.93 (QGZn.E3.2014–2016_Q3) to 25. 95% (QGZn.E1.2014–2016_Q1), respectively. Two constitutive expressing QTLs for both Fe and Zn co-mapped in this population, one on LG 2 and second one on LG 3. Inside the QTLs candidate genes such as Ferritin gene, Al3+ Transporter, K+ Transporters, Zn2+ transporters and Mg2+ transporters were identified using bioinformatics approaches. The identified QTLs and candidate genes could be useful in pearl millet population improvement programs, seed, restorer parents, and marker-assisted selection programs.

Download Full-text