QTL Validation and Development of SNP-Based High Throughput Molecular Markers Targeting a Genomic Region Conferring Narrow Root Cone Angle in Aerobic Rice Production Systems

Aerobic rice production (AP) provides potential solutions to the global water crisis by consuming less water than traditional permanent water culture. Narrow root cone angle (RCA), development of deeper rooting and associated genomic regions are key for AP adaptation. However, their usefulness depends on validation across genetic backgrounds and development of linked markers. Using three F2 populations derived from IRAT109, qRCA4 was shown to be effective in multiple backgrounds, explaining 9.3–17.3% of the genotypic variation and introgression of the favourable allele resulted in 11.7–15.1° narrower RCA. Novel kompetitive allele specific PCR (KASP) markers were developed targeting narrow RCA and revealed robust quality metrics. Candidate genes related with plant response to abiotic stress and root development were identified along with 178 potential donors across rice subpopulations. This study validated qRCA4′s effect in multiple genetic backgrounds further strengthening its value in rice improvement for AP adaptation. Furthermore, the development of novel KASP markers ensured the opportunity for its seamless introgression across pertinent breeding programs. This work provides the tools and opportunity to accelerate development of genotypes with narrow RCA through marker assisted selection in breeding programs targeting AP, which may ultimately contribute to more sustainable rice production where water availability is limited.

QTL Validation and Development of SNP-based High Throughput Molecular Markers Targeting a Genomic Region Conferring Narrow Root Cone Angle in Aerobic Rice Production Systems

BackgroundAerobic rice production (AP) is a potential solution to the imminent global water crisis as it consumes less water than traditional permanent water culture. Narrow root cone angle (RCA) and subsequent development of deeper rooting systems are considered AP adaptation traits by enabling water uptake at depth. Quantitative trait loci (QTL), such as qRCA4, contributing to RCA variation in AP systems have been previously identified. However, their usefulness depends on validation in a range of genetic backgrounds, development of associated molecular markers, and identification of possible donors in other subpopulations. Results Using three F2 bi-parental populations derived from IRAT109 crossed with three different genetic backgrounds, and genotypes with known qRCA composition, QTL validation were performed and molecular markers developed. qRCA4 was shown to be effective in multiple backgrounds, explaining 9.3-17.3% of the genotypic variation in the populations tested and the introgression of the favourable allele resulted in 11.7-15.1° narrower RCA. Novel kompetive allele specific PCR (KASP) molecular markers have been developed associated with narrow RCA. Core molecular marker quality metrics have shown robustness and breeding program specific utility of up to 83%. qRCA4 was further fine mapped into a 720 kb region. Analysis of candidate genes identified those related with plant response to abiotic stress stimulus together with root development. Available public database search found 178 potential donors representing major rice subpopulations and may be used readily by breeding programs. ConclusionThis study validated qRCA4’s effect in multiple genetic backgrounds further strengthening its value in improvement of rice genotypes for AP adaptation. Furthermore, the development of novel KASP markers has ensured the opportunity for its seamless introgression across pertinent breeding programs. Future research in metabolomic and transcriptomic analysis of QTL positive genotypes should improve the understanding of the physiological mechanisms underpinning narrow RCA and development of deeper rooting. Finally, this work provides the tools and opportunity to accelerate the development of genotypes with narrow RCA through marker assisted selection in breeding programs targeting AP, which may ultimately contribute to more sustainable rice production where water availability is limited.

Molecular breeding for combating salinity stress in sorghum: progress and prospects.

This chapter discusses current progress and prospects of molecular breeding and strategies for developing better saline-tolerant sorghum (Sorghum bicolor) varieties. Most molecular breeding techniques for salt tolerance have been carried out in controlled environments where the plants were not exposed to any variation of the surrounding environment, producing reliable results. Due to the polygenic nature of salt tolerance, the identified quantitative trait loci (QTLs) could be false QTLs. Therefore, QTL validation is important in different plant populations and field conditions. Subsequently, marker validation is important before utilizing marker-assisted selection for screening salt-tolerant plants. Combining molecular breeding with conventional breeding can hasten the development of salt-tolerant sorghum varieties.

Assessment of 16 Peanut (Arachis hypogaea L.) CSSLs Derived from an Interspecific Cross for Yield and Yield Component Traits: QTL Validation

Cultivated peanut is an allotetraploid (2n = 4× = 40) with narrow genetic diversity. In previous studies, we developed an advanced backcross quantitative trait loci (AB-QTL) population from the cross between the synthetic allotetraploid ((Arachis ipaensis × Arachis duranensis)4×) and the cultivated variety Fleur11, and mapped several quantitative trait loci (QTLs) involved in yield and yield components. We also developed a chromosome segment substitution line (CSSL) population as a way to mendelize the QTLs and analyzing their effects. In this study, 16 CSSLs were used for assessing the contribution of wild alleles in yield performance and stability across environments, as well as validating QTLs for pod and seed size. The CSSLs and the recurrent parent Fleur11, used as a check, were assessed using an alpha lattice design in three locations during two consecutive rainy seasons in Senegal, totaling six environments. Our results showed that the chromosome segments from the wild species, in general, have no yield disadvantage and contributed positive variation to yield-related traits. Most of the QTLs detected for pod and seed size in the AB-QTL on linkage groups A07, A08, A09, and B06 were also found in the CSSLs, showing that the CSSLs used in this study are accurate material for QTL validation. Several new QTLs have also been identified. Two CSSLs (12CS_031 and 12CS_069) showed consistently higher pod and seed size than Fleur11 in all environments, suggesting that the QTLs were consistent and stable. Our study opens the way for pyramiding these QTLs for peanut improvement.