Comparative transcriptome analysis between inbred and hybrids reveals molecular insights into yield heterosis of upland cotton

Abstract

Background: Utilization of heterosis has greatly enhanced the productivity of many crops worldwide. Understanding the potential molecular mechanism about how hybridization in cotton produces superior yield is critical for efficient plant breeding. Results: With the whole-genome RNA sequencing, here, high, medium, and low hybrids varying in level of yield heterosis were screened based on different years and locations field experimentation. Phenotypically, high Department showed a mean of 14% more seed cotton yield than its better parent. A total of 63 samples comprised of different squaring stage tissues of three hybrids and four their inbred parents were used to perform transcriptomic analysis. A comparison of transcriptomic differences in each hybrid parent triad revealed a higher percentage of differentially expressed genes (DEGs) in each tissue. Expression level dominance analysis exposed the majority of hybrids DEGs followed parent like expressions. Functional annotations identified an array of DEGs involved in ATP and protein binding, membrane, cell wall, mitochondrion, and protein phosphorylation. Starch and sucrose metabolism and plant hormone signal transduction pathways were most enriched in each hybrid. Further, these two pathways had most mapped DEGs on known seed cotton yield QTLs. Integration of transcriptome, QTLs, and gene co-expression network analysis raveled genes GhBZR1, GhASK8, At3g43860, GhGBSS1, GhAPL2, GhMPK4, GhPHO1, GhJAZ10, and GhCRR21 displayed a complex regulatory network of many interconnected genes. qRT-PCR of these DEGs was performed to ensure the accuracy of RNA-Seq data. Conclusions: Through genome-wide comparative transcriptome analysis, the current study provides novel insights about phenomics and genomics of heterosis in upland cotton. Our results and data resources will be useful for dissecting the molecular mechanism of yield heterosis in cotton.

Homoeolog gene expression analysis reveals novel expression biases in upland hybrid cotton under intraspecific hybridization

“…Total RNA was isolated using the Sigma Spectrum Plant Total RNA kit (Sigma-Aldrich, USA) as described by the manufacturing company. After quality checks and preparations, paired-end sequencing (300 ± 50 bp) on a secondgeneration Illumina Hiseq 4000 was performed for hybrid H and L. These sequencing details can be seen at NCBI with accession number GSE144676 (45) and GSE150052 (47). The full-length Pacbio transcriptome sequencing (Unpublished) for parental A, B, and D were used for a better comparison of homoeolog expression patterns between parents and progeny.…”

“…While the parents A and D had 44920 homologous gene pairs. These homologous sequences were used as a reference for the already published secondgeneration Illumina sequencing H and L hybrid samples (45,47). Each sample was subjected to mutation detection and speci c SNPs.…”

“…However, progress has already been achieved in the recent few years with advanced molecular research. For instance, high-throughput transcriptome sequencing is a useful technology to get accurate knowledge about global gene expressions (47,48).…”

Transcriptional regulation of maize (Zea mays) ear-length heterosis

“…Heterosis is a phenomenon in which F1 hybrid progeny exhibit superior performances compared with those of their parents [1][2][3]. It is used for hybrid crop breeding, which has greatly increased the productivity of many crops worldwide [4,5]. The successful exploitation of heterosis has also led researchers to determine its essential features.…”

“…Variation in transcriptional regulation promotes phenotypic diversity in all species [17] and, thus, is a potential source of heterosis that could explain the differences between F1 hybrids and their parental lines. Many transcriptome analyses between hybrids and inbred lines have been carried out in both maize (Zea mays) and rice (Oryza sativa), and a great number of differentially expressed genes (DEGs) were found in the F1 hybrids compared with their parents [4,[18][19][20]. Thus, heterosis was assumed to result from the global variation in gene expression between hybrids and inbred lines.…”