Tropical Plant Biology

Peres, Ana Laura Garcia Leme; Coletta, Rafael Della; Soares, José Sérgio; Menossi, Marcelo

2022 Tropical Plant Biology

doi: 10.1007/s12042-022-09313-x

One of the most common ways to study gene function is to analyze loss-of-function mutants. In polyploid species, although gene redundancy presents some advantages in nature, it offers an extra obstacle for genetic analyses due to the difficulty of obtaining loss-of-function mutants. Sugarcane presents several alleles at the same locus and the strong interaction between them contribute to the variation of phenotype and potential buffering effect, and this is one of the main challenges to study gene function in this species. Although RNA interference (RNAi) is largely used to produce loss-of-function mutants, due to the large fragments used to construct the hairpin structure, it may generate off-targets that can have confounding effect on the phenotype. The artificial micro RNA technique (amiRNA), an improved method of natural miRNA silencing, has been developed in the past years and is an useful tool for gene silencing in plants with high specificity and decreased off-target effects. In the present work we produced 26 transgenic events using amiRNA targeting the ScPDS gene, encoding a phytoene desaturase homolog. All events presented reduced expression levels of ScPDS. Although some events also showed distinguishable photobleached phenotypes, a high degree of expressivity was observed. Therefore, the use of amiRNA technique can be a good choice to silence genes in sugarcane with higher precision, and, consequently, is also a potential tool to be used in other polyploid species. However, a high number of transgenic events might be needed to achieve high levels of gene silencing.

Banerjee, Nandita; Kumar, Sanjeev; Annadurai, A.; Singh, Alok; Singh, P. K.; Singh, J.; Singh, R. K.; Kumar, Sanjeev

2022 Tropical Plant Biology

doi: 10.1007/s12042-022-09311-z

Sucrose is the prime product of sugarcane and a significant variation has been observed among different sugarcane genotypes for the time taken to initiate sucrose accumulation. High sucrose accumulation in sugarcane at early crop phase is one of the most desirable traits, since it can help in reducing its long growth cycle. This study is based on a segregating population raised in sub-tropical India, where, sucrose accumulation starts at ~ 10-month crop stage. RNA-seq data of two extreme bulks from a segregating full-sib population and its parents were used to identify differential genes and single nucleotide polymorphisms (SNPs) associated with early season high sucrose accumulation. A total of 49 common significantly differential genes were identified between high- and low- sucrose parents and bulks among which chlorophyll a-b binding protein and psaK were observed as initial points of sucrose-mediated feedback regulation. The high sucrose accumulation during early season coincided with upregulation of transcription factors (TIFY10a and ERF), and genes related to arabinogalactans, glutaredoxin, ethylene and amino acid transporters as well as downregulation of genes for solute transport (PUP, STP) and hormones (ABA and IAA). Further, six of the identified early sucrose linked DEGs, viz., ethylene-responsive transcription factor 1 (AP 2), TIFY, YUCCA, Monosaccharide transporter 2, Photosystem I reaction center subunit psaK, and chlorophyll a-b binding protein were validated for similar patterns of differential expression in a panel of sugarcane genotypes comprising the two parents and three varieties each showing early season high and low sucrose accumulation. This study was further able to identify significantly differential SNPs located pre-dominantly on several transcription factors, receptor kinases, glucuronosyltransferase, callose synthase, microRNA biogenesis complex and phytohormone action. These preliminary results provide useful insights into the role of differential genes and allelic heterozygosity in early season sucrose accumulation in sugarcane. Further confirmation of the role of these genes in early sucrose accumulation is suggested and could assist in the production of early maturing sugarcane varieties.

Fu, Danwen; Hui, Yake; Chen, Yahui; Yang, Shaohua; Gao, Feng

2022 Tropical Plant Biology

doi: 10.1007/s12042-022-09309-7

Transcription factors IbMYB1-1 had been identified involving anthocyanins biosynthesis in purple-flesh sweet potato. However, the upstream transcription factors on PIbMYB1-1 involed in anthocyanin biosynthesis had rarely been reported. In this study, the upstream transcription factors on PIbMYB1-1 were screened by yeast one-hybrid screening in purple-fleshed sweet potato storage roots. The results indicated that IbJOX4, IbWRKY1, IbSCF and IbEIN3-2 had been identified as the upstream transcription factors of PIbMYB1-1 to regulated anthocyanin biosynthesis in purple-fleshed sweet potato. The interaction between the promoters and upstream transcription factors were verified by yeast one-hybrid and luciferase reporter assays. Subcellular localization analysis indicated that IbWRKY1, IbSCF and IbEIN3-2 were nuclear proteins and functioned as transcription factors to regulate expression of downstream genes. IbWRKY1, IbSCF and IbEIN3-2 had been identified as the upstream transcription factors of PIbMYB1-1 involved in anthocyanin biosynthesis in purple-fleshed sweet potato. The results provided a possible underlying mechanism of anthocyanin biosynthesis and a potential understanding of the regulatory network in purple-fleshed sweet potato.

Adu-Gyamfi, Paul K. K.; Akpertey, Abraham; Barnor, Michael Teye; Dadzie, Abu Mustapha; Osei-Akoto, Seth; Padi, Francis

2022 Tropical Plant Biology

doi: 10.1007/s12042-022-09310-0

Flowering is one of the most critical determinants of nut tree crop yield and flower sex types that are predictive of high yields are needed to enhance the effectiveness of cashew varietal development. Under tropical and subtropical climates, cashew flowering coincides with the annual drought and could be affected by high moisture and temperature stress. The genotype × environment interaction effects on flower sex type expression of cashew has never been explored. Our current study employed a multi-environment trial established in two contrasting agro-ecological zones to elucidate the effects of genotype and environment on male, hermaphrodite and sterile flower sex type expression. Our results showed that most of the variability found were largely due to environmental influence (˃80%) and hermaphrodite and sterile flower sex types were the most sensitive. Male, hermaphrodite and sterile flower numbers ranged from 61.6–107.1, 5.6–38.7 and 1.5–14.4 per panicle respectively. The GGE Biplot model employed to analyze the interaction showed that clones SG004, SB9 and KT1 were stable for all the flower sex types. Clones that gave high number of male and hermaphrodite flowers had higher yields in suboptimal environments whereas in near optimal environments, clones that gave low number of sterile flowers had high yields. While our study highlights the benefit of employing a multi-environment trial to identify cashew clones with superior flowering characteristics to face future variability of environmental conditions attributed to global warming, the effectiveness of cashew flower sex type in predicting nut yield could vary with prevailing environmental conditions.

Pan, Zhiliang; Li, Zhiting; Zhang, Jinpeng; Bai, Shengjun; Zhao, Wei; Tong, Chunfa

2022 Tropical Plant Biology

doi: 10.1007/s12042-022-09312-y

Insertion or deletion polymorphism (InDel) is one of the main genetic variations in plant genomes. However, there are few studies on InDels across the whole genome in Populus. In this study, we investigated genome-wide InDels in Populus deltoides and Populus simonii and InDel segregation in their F1 hybrid population with restriction-site associated DNA sequencing (RAD-seq) data. A total of 119,066 InDels were identified in P. deltoides and P. simonii according to the reference genome of Populus trichocarpa, including 58,532 unique InDels in P. deltoides, 54,469 unique InDels in P. simonii, and 6,065 common InDels in both. Meanwhile, the distribution of these InDels was analyzed along chromosomes, indicating that the distribution patterns for both species were largely similar, but the average InDel density was slightly higher in P. deltoides than in P. simonii. GO annotation and enrichment analysis of those genes harboring InDels showed the same patterns between the two poplar species. It is interesting to find that the ratio (~ 46%) of the common InDels within genes to all common InDels was higher than that of the InDels within genes to all InDels in P. deltoides (~ 35%) or in P. simonii (~ 34%), possibly indicating that those InDels are more conservative between poplar species. Moreover, investigation of the InDel segregation patterns demonstrated that a large number of Mendelian InDels could be selected for genetic mapping in the F1 hybrid population. RAD-seq provides genome-wide insights into the InDel distributions in P. deltoides and P. simonii and the segregation patterns in their progeny, providing valuable genomic variation information for genetic and evolutionary studies in Populus.